Commits · 089f52cbf9bedf609b279676f1b60466b4e68688 · bioinfo / ngs_tools

May 10, 2016
- fixed dependencies · 089f52cb
  Holger Brandl authored 8 years ago
  
  089f52cb
- Merge remote-tracking branch 'remotes/origin/master' into madmax · 68beea46
  Holger Brandl authored 8 years ago
  
  68beea46
May 09, 2016
- add fpkm export to featcounts_deseq · d3488019
  Holger Brandl authored 8 years ago
  
  d3488019
May 04, 2016
- fixed typo in cleanup section · 398c04b4
  Holger Brandl authored 8 years ago
  
  398c04b4
- fixed memory and walltime · af05af46
  Holger Brandl authored 8 years ago
  
  af05af46
Apr 28, 2016
- more robust fastqc wrapper · 59b6e27e
  Holger Brandl authored 8 years ago
  
  59b6e27e
Apr 20, 2016
- revised tool to calculate genic tag proportions · 7438871a
  Holger Brandl authored 8 years ago
  
  7438871a
Apr 12, 2016
- prepared migration to furiosa · a55576b7
  Holger Brandl authored 8 years ago
  
  a55576b7
Apr 08, 2016
- updated bam correlation to work with latest deeptools. @lakshman v2.2.2 of... · 740c4ae0
  Holger Brandl authored 8 years ago
  
  updated bam correlation to work with latest deeptools. @lakshman v2.2.2 of deeptools is required now to run the star-workflow
  740c4ae0
- changed to use ngs_tools master by default · 44ecad36
  Holger Brandl authored 8 years ago
  
  44ecad36
- separated star and b1 workflows · e797a356
  Holger Brandl authored 8 years ago
  
  e797a356
Apr 06, 2016
- refined star workflow · 01b4dab6
  Holger Brandl authored 8 years ago
  
  01b4dab6
Apr 04, 2016
- fixed incorrect wall time · 342c00c5
  Holger Brandl authored 8 years ago
  
  342c00c5
Apr 01, 2016
- improved bash style · 944e014f
  Holger Brandl authored 8 years ago
  
  944e014f
Mar 24, 2016

changed to use more recent version v2.2.2 of deeptools. @lakshman to switch as... · 8fcaca17

Holger Brandl authored 8 years ago

changed to use more recent version v2.2.2 of deeptools. @lakshman to switch as well, you'll need to do a user install for your account first I guess. This is because I cant do a global installation on the cluster.

8fcaca17

Mar 21, 2016
- added cs notes · d76d3b95
  Holger Brandl authored 8 years ago
  
  d76d3b95
Mar 17, 2016
- changed default aligner wrapper to kts-version · b7921c6e
  Holger Brandl authored 9 years ago
  
  b7921c6e
- require existence of fastq inputs · 4189ca94
  Holger Brandl authored 9 years ago
  
  4189ca94
- save cached jar next to script until #5 is fixed. · 8b2eaaaf
  Holger Brandl authored 9 years ago
  
  8b2eaaaf
- added start tests · dc74d040
  Holger Brandl authored 9 years ago
  
  dc74d040
Mar 16, 2016
- rewritten scala utils in kotlin · 6b5fcd52
  Holger Brandl authored 9 years ago
  
  6b5fcd52
Mar 15, 2016
- use latest 2.5.1b STAR · def09006
  Holger Brandl authored 9 years ago
  
  def09006
- improved bash wrapper · b32e2aa7
  Holger Brandl authored 9 years ago
  
  b32e2aa7
- cont pe-aligner wrapper · ad70d502
  Holger Brandl authored 9 years ago
  
  ad70d502
- started pe-aligner wrapper · 53b1a7a1
  Holger Brandl authored 9 years ago
  
  53b1a7a1
Mar 08, 2016
- adding devtools::session_info() · aec15c2a
  Naharajan authored 9 years ago
  
  aec15c2a
- adding devtools::session_info() · ca9e1e44
  Naharajan authored 9 years ago
  
  ca9e1e44
- adding sessionInfo() · 66bbe73a
  Naharajan authored 9 years ago
  
  66bbe73a
- reverted back to clusterProfiler::bitr · fa4b3d75
  Naharajan authored 9 years ago
  
  fa4b3d75
- replaced clusterProfiler::bitr to bitr while id conversion · f5fd079e
  Naharajan authored 9 years ago
  
  f5fd079e
- Problem with plotDispEsts resolved by callign DESeq before and also loaded... · cf9fc936
  Naharajan authored 9 years ago
  
  Problem with plotDispEsts resolved by callign DESeq before and also loaded readr library for write_tsv
  cf9fc936
Mar 02, 2016
- @lakshman fixed failing star report. Now it wont mattter if bc is not yet done. · 936cea09
  Holger Brandl authored 9 years ago
  
  936cea09
- extended gc vs cov analysis · 23ceb568
  Holger Brandl authored 9 years ago
  
  23ceb568
Mar 01, 2016
- disabled chmod when building star index · 9482f08b
  Holger Brandl authored 9 years ago
  
  9482f08b
Feb 29, 2016
- @lakshman disabled chmod when creating star index · adebf72f
  Holger Brandl authored 9 years ago
  
  adebf72f
Feb 26, 2016
- adopted fc dba analysis for new data. · 4c51eecd
  Holger Brandl authored 9 years ago
  
  4c51eecd
- continued cs analysis · 1c8f2e7d
  Holger Brandl authored 9 years ago
  
  1c8f2e7d
Feb 25, 2016
- more recent version of rend.R utils · baa41e1c
  Holger Brandl authored 9 years ago
  
  baa41e1c
- tweaked bin-paths · a136d042
  Holger Brandl authored 9 years ago
  
  a136d042
Feb 24, 2016
- added mailme helper · d3a62a1e
  Holger Brandl authored 9 years ago
  
  d3a62a1e