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Dev #4

Merged
merged 235 commits into from
Dec 14, 2018
Merged

Dev #4

merged 235 commits into from
Dec 14, 2018
+5,757 −1

Commits on Oct 29, 2018

  1. convert BED file to FASTA (one per cluster)

    @renewiegandt
    renewiegandt committed Oct 29, 2018
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  2. removing redundant code

    @renewiegandt
    renewiegandt committed Oct 29, 2018
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Commits on Oct 30, 2018

  1. starting to work with custom peak calling

    @anastasiia
    anastasiia committed Oct 30, 2018
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  2. test commit

    @anastasiia
    anastasiia committed Oct 30, 2018
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  3. deleting functions that i don't need

    @anastasiia
    anastasiia committed Oct 30, 2018
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  4. saving the footprint before starting the new one

    @anastasiia
    anastasiia committed Oct 30, 2018
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  5. background changing to mean + 10%, the score for a footprint is a mea… 

    …n of all scores in this footprint
    @anastasiia
    anastasiia committed Oct 30, 2018
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  6. calculating the position with max score as the position in the middle… 

    … of first and last positions with max score
    @anastasiia
    anastasiia committed Oct 30, 2018
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  7. make save_footprint as a function on its own

    @anastasiia
    anastasiia committed Oct 30, 2018
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  8. writing to bed file

    @anastasiia
    anastasiia committed Oct 30, 2018
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  9. adding the bonus information from the original bed file to the output… 

    … footprints.bed
    @anastasiia
    anastasiia committed Oct 30, 2018
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  10. changing to the actual start and end position and not the relative on… 

    …es within a peak
    @anastasiia
    anastasiia committed Oct 30, 2018
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Commits on Nov 1, 2018

  1. Basic Nextflow structure

    @renewiegandt
    renewiegandt committed Nov 1, 2018
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  2. fixed db_channel for tomtom

    @renewiegandt
    renewiegandt committed Nov 1, 2018
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  3. adding a sorting function after the bed file was written to present i… 

    …t nice for the user
    @anastasiia
    anastasiia committed Nov 1, 2018
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  4. adding of a logger, deleting of the unsorted file after the sorting

    @anastasiia
    anastasiia committed Nov 1, 2018
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Commits on Nov 5, 2018

  1. bed_to_fasta update

    @renewiegandt
    renewiegandt committed Nov 5, 2018
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  2. Merge branch 'motif_estiamtion' of https://github.molgen.mpg.de/looso… 

    …lab/masterJLU2018 into motif_estiamtion
    @renewiegandt
    renewiegandt committed Nov 5, 2018
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  3. motif estimation docu in nf

    @renewiegandt
    renewiegandt committed Nov 5, 2018
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  4. get best motif from meme

    @renewiegandt
    renewiegandt committed Nov 5, 2018
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Commits on Nov 7, 2018

  1. Merge branch 'dev' into motif_estiamtion

    @renewiegandt
    renewiegandt committed Nov 7, 2018
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  2. added process to get best motif per meme-file

    @renewiegandt
    renewiegandt committed Nov 7, 2018
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Commits on Nov 8, 2018

  1. added uropa config

    @renewiegandt
    renewiegandt committed Nov 8, 2018
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  2. added process create_uropa_config

    @renewiegandt
    renewiegandt committed Nov 8, 2018
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  3. added scripts for part 1.2

    @renewiegandt
    renewiegandt committed Nov 8, 2018
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  4. Update: process overlap_with_known_TFBS

    @renewiegandt
    renewiegandt committed Nov 8, 2018
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Commits on Nov 12, 2018

  1. backup before changing to use a window for search

    @anastasiia
    anastasiia committed Nov 12, 2018
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  2. changing the input parameters, creating a function for searching with… 

    …in a window (not working yet)
    @anastasiia
    anastasiia committed Nov 12, 2018
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Commits on Nov 13, 2018

  1. first try with window, the problem is that in some cases the window s… 

    …lides not, i don't know why
    @anastasiia
    anastasiia committed Nov 13, 2018
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  2. the search with sliding window is done, it needs to be tested

    @anastasiia
    anastasiia committed Nov 13, 2018
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  3. need to resolve overlapping footprints

    @anastasiia
    anastasiia committed Nov 13, 2018
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  4. working on overlapping footprints

    @anastasiia
    anastasiia committed Nov 13, 2018
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Commits on Nov 19, 2018

  1. added script for process 'footprint_extraction'

    @renewiegandt
    renewiegandt committed Nov 19, 2018
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  2. added script for process 'footprint_extraction'

    @renewiegandt
    renewiegandt committed Nov 19, 2018
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Commits on Nov 20, 2018

  1. adding one dictionary for each peak, so that we can easily look for p… 

    …ossibly overlaps
    @anastasiia
    anastasiia committed Nov 20, 2018
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  2. Add files via upload

    @JannikHamp
    JannikHamp committed Nov 20, 2018
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  3. Add files via upload

    @JannikHamp
    JannikHamp committed Nov 20, 2018
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  4. Update README.md

    @JannikHamp
    JannikHamp committed Nov 20, 2018
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  5. Update README.md

    @JannikHamp
    JannikHamp committed Nov 20, 2018
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  6. deleting of overlaps is working

    @anastasiia
    anastasiia committed Nov 20, 2018
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Commits on Nov 21, 2018

  1. the number of peaks and the number of footprints is printed with help… 

    … of logger
    @anastasiia
    anastasiia committed Nov 21, 2018
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  2. adding the possibility for user to chose how many percent to add to t… 

    …he background
    @anastasiia
    anastasiia committed Nov 21, 2018
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  3. deleting of an unused function

    @anastasiia
    anastasiia committed Nov 21, 2018
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  4. using the output file as parameter as well as rounding of the scores

    @anastasiia
    anastasiia committed Nov 21, 2018
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  5. deleting of unused imports and explaining why the other imports are n… 

    …eeded
    @anastasiia
    anastasiia committed Nov 21, 2018
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  6. final commenting for the important functions in the script

    @anastasiia
    anastasiia committed Nov 21, 2018
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  7. deleting of unused code

    @anastasiia
    anastasiia committed Nov 21, 2018
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Commits on Nov 28, 2018

  1. update, working with unmerged motif files now

    @JannikHamp
    JannikHamp committed Nov 28, 2018
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Commits on Nov 29, 2018

  1. update, bugfix output parameter error

    @JannikHamp
    JannikHamp committed Nov 29, 2018
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  2. added filter for small clusters

    @renewiegandt
    renewiegandt committed Nov 29, 2018
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  3. changed tomtom/glam2 parameters; added min_seq parameter

    @renewiegandt
    renewiegandt committed Nov 29, 2018
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  4. Merge pull request #1 from loosolab/motif_estiamtion 

    Motif estiamtion
    @renewiegandt
    renewiegandt committed Nov 29, 2018
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Commits on Dec 3, 2018

  1. Merge branch 'dev' into peak_calling

    petrokvitka authored and petrokvitka committed Dec 3, 2018
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  2. move the call_peaks.py script to the bin directory

    petrokvitka authored and petrokvitka committed Dec 3, 2018
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  3. control changes

    @anastasiia
    anastasiia committed Dec 3, 2018
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  4. adding the environment for the peak calling

    @anastasiia
    anastasiia committed Dec 3, 2018
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  5. editing of the commits

    @anastasiia
    anastasiia committed Dec 3, 2018
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  6. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  7. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  8. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  9. added yaml file for conda enviroment

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  10. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  11. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  12. added nextflow configuration files

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  13. added parameter to config files

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  14. update config file

    @anastasiia
    anastasiia committed Dec 3, 2018
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  15. adding dependencies needed for call_peak.py

    @anastasiia
    anastasiia committed Dec 3, 2018
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  16. final changes in comments

    @anastasiia
    anastasiia committed Dec 3, 2018
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  17. added enviroment parameter

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  18. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  19. Merge branch 'peak_calling' into dev

    @anastasiia
    anastasiia committed Dec 3, 2018
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  20. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @anastasiia
    anastasiia committed Dec 3, 2018
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  21. removed redundant parameter

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  22. added conda; bed input

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  23. added parameter to pipeline

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  24. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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  25. Update README.md

    @renewiegandt
    renewiegandt committed Dec 3, 2018
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Commits on Dec 4, 2018

  1. delete unused logger statements

    @anastasiia
    anastasiia committed Dec 4, 2018
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  2. overlap_with_known_TFBS: input/output changes

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  3. add bed sequence reduction script

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  4. add cdhit wrapper script

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  5. Inital commit ! -> Migration to new project

    basti committed Dec 4, 2018
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  6. Update .ignore

    basti committed Dec 4, 2018
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  7. Create README.md

    @SebastianBeyvers
    SebastianBeyvers committed Dec 4, 2018
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  8. fixed cdhit wrapper description

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  9. Readme aktualisier

    basti committed Dec 4, 2018
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  10. Check for local Folders

    basti committed Dec 4, 2018
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  11. update the name of log-file

    @anastasiia
    anastasiia committed Dec 4, 2018
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  12. update the name of the log-file

    @anastasiia
    anastasiia committed Dec 4, 2018
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  13. renaming channels

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  14. Merge branch 'dev' into motif_estiamtion

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  15. remove sequences below threshold (not above)

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  16. added parameter to config

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  17. finished create_GTF

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  18. show progressbar even in non interactive context

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  19. merge gtf to motif

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  20. moved Modules to bin

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  21. Delete .gitignore

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  22. Changed config locations

    basti committed Dec 4, 2018
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  23. Added Dev to new local branch

    basti committed Dec 4, 2018
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  24. changed resultpath

    basti committed Dec 4, 2018
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  25. Added Dev to new local branch

    basti committed Dec 4, 2018
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  26. added documentation

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  27. added cluster dependencies

    @HendrikSchultheis
    HendrikSchultheis committed Dec 4, 2018
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  28. Changed Paths

    basti committed Dec 4, 2018
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  29. Merge remote-tracking branch 'origin/dev_gtfdev' into dev_gtfdev

    basti committed Dec 4, 2018
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  30. Changed Paths

    basti committed Dec 4, 2018
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  31. Changed Paths

    basti committed Dec 4, 2018
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  32. minor changes

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  33. Merge branch 'dev_gtfdev' into dev

    basti committed Dec 4, 2018
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  34. Changed Paths

    basti committed Dec 4, 2018
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  35. Changed Paths

    basti committed Dec 4, 2018
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  36. moved config for gtf creation

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  37. Fixed: "No Module named bin Error"

    basti committed Dec 4, 2018
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  38. Merge remote-tracking branch 'origin/dev' into dev

    basti committed Dec 4, 2018
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  39. Fixed: "No Module named bin Error" V2

    basti committed Dec 4, 2018
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  40. Fixed: "No Module named bin Error" V2

    basti committed Dec 4, 2018
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  41. Fixed: "No Module named bin Error" V2

    basti committed Dec 4, 2018
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  42. Fixed: "No Module named bin Error" V2

    basti committed Dec 4, 2018
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  43. Fixed: "No Module named bin Error" V2

    basti committed Dec 4, 2018
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  44. Update masterenv.yml

    @renewiegandt
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  45. Merge pull request #2 from loosolab/cluster 

    Cluster
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  46. Update masterenv.yml

    @renewiegandt
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  47. Fixed: "Paths" V2

    basti committed Dec 4, 2018
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  48. Merge remote-tracking branch 'origin/dev' into dev

    basti committed Dec 4, 2018
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  49. added clustering + reducing

    @renewiegandt
    renewiegandt committed Dec 4, 2018
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  50. added parameter

    @renewiegandt
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  51. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
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Commits on Dec 5, 2018

  1. fixed minimum sequence length and added check

    @HendrikSchultheis
    HendrikSchultheis committed Dec 5, 2018
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  2. implemented minoverlap_kmer & minoverlap_motif

    @HendrikSchultheis
    HendrikSchultheis committed Dec 5, 2018
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  3. better docu; reorder data in reduce_kmer()

    @HendrikSchultheis
    HendrikSchultheis committed Dec 5, 2018
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  4. Rscript first line changes

    @JannikHamp
    JannikHamp committed Dec 5, 2018
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  5. Delete README.md

    @JannikHamp
    JannikHamp committed Dec 5, 2018
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  6. Changed ResultPath

    basti committed Dec 5, 2018
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  7. Changed ResultPath

    basti committed Dec 5, 2018
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  8. Changed ResultPath

    basti committed Dec 5, 2018
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  9. added progress messages; thread param; documentation

    @HendrikSchultheis
    HendrikSchultheis committed Dec 5, 2018
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  10. merge dev

    @JannikHamp
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  11. moved scripts to bin

    @renewiegandt
    renewiegandt committed Dec 5, 2018
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  12. Delete .gitignore

    @renewiegandt
    renewiegandt committed Dec 5, 2018
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  13. added parameter to yaml

    @renewiegandt
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  14. added tfbsscan.py to bin

    @renewiegandt
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  15. added and moved parameter in config

    @renewiegandt
    renewiegandt committed Dec 5, 2018
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  16. added default parameter in script

    @renewiegandt
    renewiegandt committed Dec 5, 2018
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  17. moved uropa.config to config dir

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  18. added help message

    @renewiegandt
    renewiegandt committed Dec 5, 2018
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Commits on Dec 6, 2018

  1. added new config file 'filter_unknown_motifs'

    @renewiegandt
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  2. implemented motif_occurence for cutoff computation

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  3. threads = 0 for all cores to match cd-hit

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  4. help message

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  5. Update README.md

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  6. Update README.md

    @renewiegandt
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  7. Update README.md

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  8. Update README.md

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  9. added more cdhit parameter

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  10. changed type of motif_occurence to double

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  11. renamed ignore_strand to strand

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  12. new clustering parameter added

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  13. Merge remote-tracking branch 'origin/dev' into cluster 

    # Conflicts:
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    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  14. Update README.md

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  15. fixed ambiguous flags

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  16. fixed ambiguous flags + nameing bug in find_kmer_regions

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  17. removed param threads

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  18. added parameter to list and description

    @HendrikSchultheis
    HendrikSchultheis committed Dec 6, 2018
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  19. Merge pull request #3 from loosolab/cluster 

    Cluster
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    renewiegandt committed Dec 6, 2018
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  20. minor changes

    @renewiegandt
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  21. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  22. removed debug code

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  23. bugfixing

    @JannikHamp
    JannikHamp committed Dec 6, 2018
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  24. Update README.md

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  25. ...

    @JannikHamp
    JannikHamp committed Dec 6, 2018
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  26. fixing

    @JannikHamp
    JannikHamp committed Dec 6, 2018
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  27. fixing

    @JannikHamp
    JannikHamp committed Dec 6, 2018
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  28. fixing

    @JannikHamp
    JannikHamp committed Dec 6, 2018
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  29. fixed failed merge

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  30. fixed failed merge

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  31. fixed failed merge

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  32. minor fix

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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  33. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
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  34. added process merge_meme

    @renewiegandt
    renewiegandt committed Dec 6, 2018
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Commits on Dec 7, 2018

  1. removed typo

    @renewiegandt
    renewiegandt committed Dec 7, 2018
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  2. setting up prozesses for motif clustering

    @renewiegandt
    renewiegandt committed Dec 7, 2018
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  3. added script merge_similar_clusters.R

    @renewiegandt
    renewiegandt committed Dec 7, 2018
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Commits on Dec 8, 2018

  1. added motif clustering

    @renewiegandt
    renewiegandt committed Dec 8, 2018
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  2. Update README.md

    @renewiegandt
    renewiegandt committed Dec 8, 2018
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  3. Update README.md

    @renewiegandt
    renewiegandt committed Dec 8, 2018
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Commits on Dec 10, 2018

  1. Update compareBed.sh

    @JannikHamp
    JannikHamp committed Dec 10, 2018
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  2. minor changes

    @renewiegandt
    renewiegandt committed Dec 10, 2018
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  3. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 10, 2018
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  4. Implemented --dir parameter for remote data directory

    basti committed Dec 10, 2018
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  5. correcting some errors

    @anastasiia
    anastasiia committed Dec 10, 2018
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  6. Update README.md

    @renewiegandt
    renewiegandt committed Dec 10, 2018
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  7. adding comment about the footprints_extraction

    @anastasiia
    anastasiia committed Dec 10, 2018
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  8. Update README.md

    @renewiegandt
    renewiegandt committed Dec 10, 2018
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  9. improvement of parameters for my part

    @anastasiia
    anastasiia committed Dec 10, 2018
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  10. improve parameters for my part once more

    @anastasiia
    anastasiia committed Dec 10, 2018
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  11. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 10, 2018
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  12. help message fix

    @renewiegandt
    renewiegandt committed Dec 10, 2018
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  13. Updated README. 

    Added CrossMap functionality.
Added mm9 and hg19 support.
    basti committed Dec 10, 2018
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  14. Merge remote-tracking branch 'origin/dev' into dev 

    # Conflicts:
#	masterenv.yml
    basti committed Dec 10, 2018
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  15. Updated README.

    basti committed Dec 10, 2018
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  16. Update Readme

    @SebastianBeyvers
    SebastianBeyvers committed Dec 10, 2018
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  17. Added more comments!

    basti committed Dec 10, 2018
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  18. Merge remote-tracking branch 'origin/dev' into dev

    basti committed Dec 10, 2018
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  19. Changed Readme

    basti committed Dec 10, 2018
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Commits on Dec 11, 2018

  1. Changed Readme and updated mm_config

    basti committed Dec 11, 2018
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  2. data error fixed

    basti committed Dec 11, 2018
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  3. error in output fixed

    basti committed Dec 11, 2018
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Commits on Dec 12, 2018

  1. Fixed small bug in output formatting for mm10/mm9

    basti committed Dec 12, 2018
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  2. updated README

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  3. minor bugfix

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  4. added T parameter for sorting

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  5. removed parameter

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  6. tfbsscan optional; minor fixes/changes

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  7. fixed yml-file

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  8. minor changes

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  9. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 12, 2018
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  10. Update README.md

    @renewiegandt
    renewiegandt committed Dec 12, 2018
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Commits on Dec 13, 2018

  1. we do not need this env

    @anastasiia
    anastasiia committed Dec 13, 2018
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  2. Update README.md

    @renewiegandt
    renewiegandt committed Dec 13, 2018
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  3. Update merge.R

    @JannikHamp
    JannikHamp committed Dec 13, 2018
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  4. check prameters; minor fixes

    @renewiegandt
    renewiegandt committed Dec 13, 2018
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  5. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 13, 2018
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  6. Update README.md

    @renewiegandt
    renewiegandt committed Dec 13, 2018
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  7. Update README.md

    @renewiegandt
    renewiegandt committed Dec 13, 2018
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Commits on Dec 14, 2018

  1. Fixed bug in formatting (gff vs gtf). Converted feature description t… 

    …o lowercase.
    basti committed Dec 14, 2018
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  2. fixes

    @renewiegandt
    renewiegandt committed Dec 14, 2018
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  3. resolve merge conflict

    @renewiegandt
    renewiegandt committed Dec 14, 2018
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  4. fix

    @renewiegandt
    renewiegandt committed Dec 14, 2018
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  5. removed echo true from process

    @renewiegandt
    renewiegandt committed Dec 14, 2018
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  6. Readme formatted

    @SebastianBeyvers
    SebastianBeyvers committed Dec 14, 2018
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  7. $"motifs" falsch -> "$motifs" richtig :)

    @JannikHamp
    JannikHamp committed Dec 14, 2018
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  8. minor fix

    @renewiegandt
    renewiegandt committed Dec 14, 2018
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  9. Merge branch 'dev' of https://github.molgen.mpg.de/loosolab/masterJLU… 

    …2018 into dev
    @renewiegandt
    renewiegandt committed Dec 14, 2018
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  10. added info for FilterMotifs.stats

    @JannikHamp
    JannikHamp committed Dec 14, 2018
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