diff --git a/docs/genesets.md b/docs/genesets.md index 800ba70..f849c67 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)[http://www.broadinstitute.org/gsea/msigdb/index.jsp]. \ 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/regions.md b/docs/regions.md index 1fe6295..d84a78b 100644 --- a/docs/regions.md +++ b/docs/regions.md @@ -1,7 +1,8 @@ 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) + +*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: diff --git a/docs/test.html b/docs/test.html deleted file mode 100644 index 754ea05..0000000 --- a/docs/test.html +++ /dev/null @@ -1,38 +0,0 @@ - - -
- - - -ADMIRE is a semi-automatic analysis pipeline and visualization tool for Infinium HumanMethylation450K Chips.
-Use ADMIRE online: bioinformatics.mpi-bn.mpg.de
-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.
-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.
-If you are having issues, please feel free to send an e-mail to Jens Preußner (jens.preussner@mpi-bn.mpg.de).
-The project is licensed under the MIT license.
- -