Commits · 68beea46db89bb3bc5b4e8c1cf778a7c17736df1 · bioinfo / ngs_tools

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 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 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
- 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
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
- rreplace mysub with jl submit · ae3d1340
  Holger Brandl authored 9 years ago
  
  ae3d1340
Feb 23, 2016
- added backward compatibility wrappers for old shell cluster utils · 815f3301
  Holger Brandl authored 9 years ago
  
  815f3301
Feb 04, 2016
- impl gc vs coverage correlation · ca8e7c8c
  Holger Brandl authored 9 years ago
  
  ca8e7c8c
Feb 01, 2016
- disabled duplicated export of diffex genes · f047009a
  Holger Brandl authored 9 years ago
  
  f047009a
Jan 26, 2016
- cont pathway visualization · 2499fcbf
  Holger Brandl authored 9 years ago
  
  2499fcbf
Jan 07, 2016
- fixed intercept parameter name when using geom_vline · 4a9b12be
  Holger Brandl authored 9 years ago
  
  4a9b12be
Jan 06, 2016
- fixed directionality assignment · 273a9193
  Holger Brandl authored 9 years ago
  
  273a9193
Jan 05, 2016
- added spin.R to common dependencies · 4f5cf3ff
  Holger Brandl authored 9 years ago
  
  4f5cf3ff
Jan 04, 2016
- fixed relative links to tables; added jl to PATH · 5d29433a
  Holger Brandl authored 9 years ago
  
  5d29433a
Dec 18, 2015
- modernized final annotation filtering · ffe0955f
  Holger Brandl authored 9 years ago
  
  ffe0955f
Dec 16, 2015
- converted star index creation to use jl · 98ea751d
  Holger Brandl authored 9 years ago
  
  98ea751d