Resolve "Add in current chip-analysis functionality." (!18) · Merge requests · BICF / Astrocyte / chipseq_analysis

Merged Resolve "Add in current chip-analysis functionality."

15_Annotation_diff_bind into master

Merged Venkat Malladi requested to merge 15_Annotation_diff_bind into master 6 years ago

Jan 10, 2019
- Make csv to tsv. · ad8a4c25
  Venkat Malladi authored 6 years ago
  
  ad8a4c25
- reduce to one page. · 29ea563e
  Venkat Malladi authored 6 years ago
  
  29ea563e
- Fix test peaks. · 1ca8372e
  Venkat Malladi authored 6 years ago
  
  1ca8372e
Jan 09, 2019
- Update configuration. · 96069f62
  Venkat Malladi authored 6 years ago
  
  96069f62
- Fix annotate length. · b1dbf288
  Venkat Malladi authored 6 years ago
  
  b1dbf288
- Fix number of peaks. · 785478ce
  Venkat Malladi authored 6 years ago
  
  785478ce
Jan 08, 2019
- Fixed test data and test output. · 200ded13
  Venkat Malladi authored 6 years ago
  
  200ded13
- Update number of peaks. · 7f082ef8
  Venkat Malladi authored 6 years ago
  
  7f082ef8
Jan 07, 2019
- Fix yaml error. · 12a58779
  Venkat Malladi authored 6 years ago
  
  12a58779
- Update staging to be unit, single and multiple. · 9b00fd0b
  Venkat Malladi authored 6 years ago
  
  9b00fd0b
- Fix paired-end tests. · 3631108c
  Venkat Malladi authored 6 years ago
  
  3631108c
- Fix what tests are run and the testing output. · 6fddf146
  Venkat Malladi authored 6 years ago
  
  6fddf146
Jan 06, 2019
- verify that output directory doesn't exist. · d6dd0596
  Venkat Malladi authored 6 years ago
  
  d6dd0596
- Fix test options and files that should be moved over. · 3a0ac094
  Venkat Malladi authored 6 years ago
  
  3a0ac094
- fix missing genome params and annotate peaks syntax. · cde5c10a
  Venkat Malladi authored 6 years ago
  
  cde5c10a
- Reslove merge conflicts. · 78b410c7
  Venkat Malladi authored 6 years ago
  
  78b410c7
- Remove test code. · ac16a48e
  Venkat Malladi authored 6 years ago
  
  ac16a48e
- Change output of diffPeaks design file. · 83e1537d
  Venkat Malladi authored 6 years ago
  
  83e1537d
Jan 05, 2019
- Test for new unique experiment determination. · 4a27bcf5
  Venkat Malladi authored 6 years ago
  
  4a27bcf5
- Change order of process. Made diffPeaks a when opperative. · 92096435
  Venkat Malladi authored 6 years ago
  
  92096435
- Change test lenght of output. · 6b3c190b
  Venkat Malladi authored 6 years ago
  
  6b3c190b
Jan 04, 2019
- remove annotate peak vennpie and update test. · afa3bbee
  Venkat Malladi authored 6 years ago
  
  afa3bbee
- Fix memechip output directoires. · 673c0718
  Venkat Malladi authored 6 years ago
  
  673c0718
Dec 27, 2018
- Fix merge conflicts. · 6ed06727
  Venkat Malladi authored 6 years ago
  
  6ed06727
- Add test for motif search output. · 1a61363d
  Venkat Malladi authored 6 years ago
  
  1a61363d
- Check differential peaks. · d84a3b62
  Venkat Malladi authored 6 years ago
  
  d84a3b62
- Remove testing design string. · eea9ab16
  Venkat Malladi authored 6 years ago
  
  eea9ab16
- Fix tests so they run on single end and paired end. · c508559b
  Venkat Malladi authored 6 years ago
  
  c508559b
- Fix motif search and limit number of peaks. · 813fb41d
  Venkat Malladi authored 6 years ago
  
  813fb41d
Dec 26, 2018
- Remove output and rename touched files. · 6de1721c
  Venkat Malladi authored 6 years ago
  
  6de1721c
- Update script name, R version and end result. · 6f6aa9d5
  Venkat Malladi authored 6 years ago
  
  6f6aa9d5
- Fix program description. · 954ecd5f
  Venkat Malladi authored 6 years ago
  
  954ecd5f
- Change R version and output. · e7b72cfb
  Venkat Malladi authored 6 years ago
  
  e7b72cfb
Dec 25, 2018
- Fix our file name · 0f2a8f86
  Venkat Malladi authored 6 years ago
  
  0f2a8f86
- Termite annodb · 931b9086
  Venkat Malladi authored 6 years ago
  
  931b9086
Dec 24, 2018
- Add missing libraries · 16b629be
  Venkat Malladi authored 6 years ago
  
  16b629be
- Remove extra parathesis · c6374f18
  Venkat Malladi authored 6 years ago
  
  c6374f18
- Test annotate peaks. · ea9dc8e6
  Venkat Malladi authored 6 years ago
  
  ea9dc8e6
- Add in paired end test data. · 7bddefc4
  Venkat Malladi authored 6 years ago
  
  7bddefc4
- Added in test data for comparisions. · cf982549
  Venkat Malladi authored 6 years ago
  
  cf982549
Dec 17, 2018
- Defaulted to zcat instead of unzip file. · ec737360
  Venkat Malladi authored 6 years ago
  
  ec737360
Dec 16, 2018
- Update motif search scripts to meet new python standards · e2f0afca
  Venkat Malladi authored 6 years ago
  
  e2f0afca
- Merge branch 'master' into 15_Annotation_diff_bind · fa33cd9b
  Venkat Malladi authored 6 years ago
  
  fa33cd9b
Oct 31, 2018
- Revert main · acebeb68
  Venkat Malladi authored 6 years ago
  
  acebeb68
- Fix current chip-seq pipeline. · 2d887a76
  Venkat Malladi authored 6 years ago
  
  2d887a76
Aug 14, 2018
- Add proper syntax. · f44b0481
  Venkat Malladi authored 6 years ago
  
  f44b0481
- Fix syntax and readlines. · 6a2d842c
  Venkat Malladi authored 6 years ago
  
  6a2d842c
- New test. · a0568644
  Venkat Malladi authored 6 years ago
  
  a0568644
- Fix reading experiment files. · 3df606ed
  Venkat Malladi authored 6 years ago
  
  3df606ed
- Change to just size. · c0d36466
  Venkat Malladi authored 6 years ago
  
  c0d36466
- Change to new conventions. · 035156b7
  Venkat Malladi authored 6 years ago
  
  035156b7
- Upgrade nextflow version. · 998c2bd7
  Venkat Malladi authored 6 years ago
  
  998c2bd7
- Fix channel. · eea2f6f3
  Venkat Malladi authored 6 years ago
  
  eea2f6f3
- Add in paired end tests for calling peaks. · e3a0a043
  Venkat Malladi authored 6 years ago
  
  e3a0a043
Aug 13, 2018
- Fix diffBind output. · ffbb85b0
  Venkat Malladi authored 6 years ago
  
  ffbb85b0
- Add in Resume option. · fe188a10
  Venkat Malladi authored 6 years ago
  
  fe188a10
Aug 11, 2018
- Hardcode to 2. · 2b4d340c
  Venkat Malladi authored 6 years ago
  
  2b4d340c
- Fix syntax. · c9b2fa2e
  Venkat Malladi authored 6 years ago
  
  c9b2fa2e
- Fix diffbind. · 1bc7294b
  Venkat Malladi authored 6 years ago
  
  1bc7294b
- First pass at updating documentation. · 7795c421
  Venkat Malladi authored 6 years ago
  
  7795c421
- Fix library issues for R. · 0e768b53
  Venkat Malladi authored 6 years ago
  
  0e768b53
- Update samtools. · 805590f5
  Venkat Malladi authored 6 years ago
  
  805590f5
- Add in experiment qc for paired-end data. · faad8b58
  Venkat Malladi authored 6 years ago
  
  faad8b58
- Add in test cross-correlation. · 7bbb0bbd
  Venkat Malladi authored 6 years ago
  
  7bbb0bbd
- Assert paired end files exist. · a8c27eae
  Venkat Malladi authored 6 years ago
  
  a8c27eae
- Add in paired-end filter test. · 58b92f5d
  Venkat Malladi authored 6 years ago
  
  58b92f5d
- Add in paried-end reads test for alignment. · e9328bd2
  Venkat Malladi authored 6 years ago
  
  e9328bd2
- Add in trim reads paired end. · c7a09e6c
  Venkat Malladi authored 6 years ago
  
  c7a09e6c
Jul 25, 2018
- Test · 0b4b9966
  Venkat Malladi authored 6 years ago
  
  0b4b9966
- Fix syntax · b8564cfe
  Venkat Malladi authored 6 years ago
  
  b8564cfe
- Fix syntax · 46e7e5e3
  Venkat Malladi authored 6 years ago
  
  46e7e5e3
- Fix syntax · f6184625
  Venkat Malladi authored 6 years ago
  
  f6184625
- Fix path · 11628381
  Venkat Malladi authored 6 years ago
  
  11628381
- Fix readlines. · f4e07f44
  Venkat Malladi authored 6 years ago
  
  f4e07f44
- Fix workflow. · 2ede9219
  Venkat Malladi authored 6 years ago
  
  2ede9219
- add in motif search. · 5198436d
  Venkat Malladi authored 6 years ago
  
  5198436d
Jul 24, 2018
- Covert csv to tsv. · 65bc6b76
  Venkat Malladi authored 6 years ago
  
  65bc6b76
- Add in differntial binding peaks. · 7b67dda5
  Venkat Malladi authored 6 years ago
  
  7b67dda5
- Update annotation script. · 7deea97e
  Venkat Malladi authored 6 years ago
  
  7deea97e
- Merge branch 'master' into 15_Annotation_diff_bind · 0620eafd
  Venkat Malladi authored 6 years ago
  
  0620eafd
May 08, 2018
- First start at adding annotations. · a858f1c3
  Venkat Malladi authored 6 years ago
  
  a858f1c3

Resolve "Add in current chip-analysis functionality."

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