diff --git a/docs/custom.md b/docs/custom.md index b84d2df..fef02ef 100644 --- a/docs/custom.md +++ b/docs/custom.md @@ -1,4 +1,14 @@ ADMIRE is also able to process a tab-separated sample definition file, with the following columns: + +column | explanation +-------|------------ +sample_id | an arbitrary sample identifier. Note that corresponding green and red channel files need the same identifier. +file | relative or absolute path of a red or green channel idat file. +channel | indicates whether the file is from the red or green channel (can be *Red* or *Grn*). +sample_group | an arbitrary string identifying the sample group of the sample. + +For example, the sample definition file could look like: + ``` sample_id file channel sample_group 1 8769527070/8769527070_R01C01_Grn.idat Grn control @@ -7,5 +17,5 @@ sample_id file channel sample_group 3 8769527070/8769527070_R02C01_Red.idat Red treatment ``` -ADMIRE can then be called with `admire -s sample_definition.txt` and will look the *.idat files specified in the sample definition file. +ADMIRE can then be called with `admire -s sample_definition.txt` and will look for the \*.idat files specified in the sample definition file. \ No newline at end of file diff --git a/docs/genesets.md b/docs/genesets.md index 592a97b..800ba70 100644 --- a/docs/genesets.md +++ b/docs/genesets.md @@ -1 +1 @@ -Gene sets can be given with admire -g geneset1 -g geneset2 .... Gene set files should be in *.gmt format, as provided by MSigDB [4]. \ No newline at end of file +Gene sets can be given with `admire -g geneset1 -g geneset2 ...`. Gene set files should be in *.gmt format, as provided by (MSigDB)[http://www.broadinstitute.org/gsea/msigdb/index.jsp]. \ No newline at end of file diff --git a/docs/hiscan.md b/docs/hiscan.md index a4dd8d0..f545814 100644 --- a/docs/hiscan.md +++ b/docs/hiscan.md @@ -7,4 +7,4 @@ To use the files generated by the scanner system with ADMIRE, all file directori ADMIRE can then be called with `admire -c SampleSheet.csv -z compressFileName.tar.gz` -*Hint*: ADMIRE can also read files ending on *.zip or *.tbz2. \ No newline at end of file +*Hint*: ADMIRE can also read files ending on \*.tar.gz, \*.tgz or \*.tbz2. \ No newline at end of file diff --git a/docs/index.md b/docs/index.md index 821f086..60a3729 100644 --- a/docs/index.md +++ b/docs/index.md @@ -26,7 +26,9 @@ Features How to cite? ------------ -Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. *???* (**2015**) when using admire in your work. +Please cite the paper describing ADMIRE when using the web service or command line version in your research: + +Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay. *???* (**2015**) when using admire in your work. Contribute ---------- diff --git a/docs/parameters.md b/docs/parameters.md new file mode 100644 index 0000000..8a3ed3d --- /dev/null +++ b/docs/parameters.md @@ -0,0 +1,28 @@ +Here we list all current parameters for command-line usage and their explanation: + +``` +Usage: admire [options] + +Available options: +-c | Comma separated sample definition file (SampleSheet.csv) +-s | Tab separated sample definition file (design.txt) +-z | Compressed input of idat files (requires -c). +-e | Create quality control report in PDF +-r | Region file in bed format (regions.bed), use multiple -r parameters to calculate for multiple region files +-p | Detection p-value to exclude probes prior to analysis (0.01) +-t | Exclude probes where more than t% samples failed according to the detection p-value. (0.4) +-n | Normalization method (fn,swan,noob,illumina,raw,quantile) +-b | In case of functional normalization, skip noob background correction step +-d | In case of noob or functional normalization, skip dye correction step +-f | In case of quantile normalization, skip fixing outliers prior to analysis +-l | In case of quantile normalization, label samples as bad if their median signals are below a given value (10.5) +-m | In case of quantile normalization, remove bad samples +-q | Q-value cutoff for multiple testing correction (0.05) +-i | Render advanced plots for the best i regions (20) +-g | Gene set file for enrichment analysis, use multiple -g parameters to calculate enrichment over many gene sets +-o | tar-gz compress output into file given +-h | shows this help message +-v | shows version information + +Options -c and -s are mutually exclusive. +``` \ No newline at end of file diff --git a/docs/regions.md b/docs/regions.md index 8030ee1..1fe6295 100644 --- a/docs/regions.md +++ b/docs/regions.md @@ -1 +1,12 @@ -Custom genomic regions should be provided in BED format and can be given by admire -r regions1.bed -r regions2.bed ... \ No newline at end of file +Custom genomic regions should be provided in BED format and can be given by `admire -r regions1.bed -r regions2.bed ...`. + +*Hint*: Use multiple `-r` parameters to analyse more than one region at a time. +*Hint*: The BED format is described [here](http://www.ensembl.org/info/website/upload/bed.html) + +To enable the Gene Set Enrichment Analysis for a certain bed file, include a *gene_name* property in column 4 of the bed file: + +``` +chr1 213941196 213942363 gene_name=gene1 +chr1 213942363 213943530 gene_name=gene2 +chr1 213943530 213944697 gene_name=gene3 +``` \ No newline at end of file diff --git a/docs/test.html b/docs/test.html new file mode 100644 index 0000000..754ea05 --- /dev/null +++ b/docs/test.html @@ -0,0 +1,38 @@ + + + + + + + + + + +

Welcome to the ADMIRE documentation

+

ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.

+

Use ADMIRE online: bioinformatics.mpi-bn.mpg.de

+

Overview and Objective

+

DNA methylation at cytosine nucleotides constitutes epigenetic gene regulation impacting cellular development and the stage of a disease. Besides whole genome bisulfit sequencing, Illumina HumanMethylation450K Assays represent a versatile and cost-effective tool to investigate changes of methylation patterns at CpG sites. ADMIRE was developed as an open source, semi-automatic analysis pipeline and visualization tool for Illumina HumanMethylation450K Assays.

+

Features

+ +

How to cite?

+

Please cite Preussner J, Bayer J, Kuenne C and Looso M. ADMIRE: Analysis and visualization of differential methylation in genomic regions using Infinium HumanMethylation450K Chips. ??? (2015) when using admire in your work.

+

Contribute

+ +

Support

+

If you are having issues, please feel free to send an e-mail to Jens Preußner (jens.preussner@mpi-bn.mpg.de).

+

License

+

The project is licensed under the MIT license.

+ + diff --git a/mkdocs.yml b/mkdocs.yml index 81566ff..4dab128 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,4 +1,6 @@ site_name: ADMIRE +site_description: 'Analysis and visualization of differential methylation in genomic regions using the Infinium HumanMethylation450 Assay.' +site_author: 'Jens Preussner, Julia Bayer, Carsten Kuenne, Mario Looso' repo_url: https://github.molgen.mpg.de/loosolab/admire repo_name: 'GitHub' pages: @@ -13,5 +15,6 @@ pages: - 'Custom input': 'custom.md' - 'Genomic regions' : 'regions.md' - 'Gene sets' : 'genesets.md' + - 'Available parameters' : 'parameters.md' - Output: 'output.md' - 'MIT License': 'license.md' \ No newline at end of file