Commits · master · Blaise LI / bioinfo_utils

Jul 10, 2024
- Make local rule compatible with snakemake v5. · fec62b53
  Blaise Li authored 1 year ago
  
  fec62b53
Apr 21, 2023
- Gene id conversion fix in all pipelines. · 54f1e09c
  Blaise Li authored 2 years ago
  
  54f1e09c
Oct 05, 2020
- Trying to have params set in wrapper. · ee182bc8
  Blaise Li authored 4 years ago
  
  ee182bc8
- Can't use generator as input function in wrapper. · 33564325
  Blaise Li authored 4 years ago
  
  33564325
- Typo. · fc322b26
  Blaise Li authored 4 years ago
  
  fc322b26
- Getting mapping parameters from test runs. · bbf0883b
  Blaise Li authored 4 years ago
  
  bbf0883b
- Ensuring read size classes are merged. · 5eb40a44
  Blaise Li authored 4 years ago
  5eb40a44
Oct 02, 2020
- Adapting TPM and RPM counting from RNA-seq. · 28d6e34e
  Blaise Li authored 4 years ago
  
  28d6e34e
Oct 01, 2020
- Merging size classes in iCLIP data. · 38c641d1
  Blaise Li authored 4 years ago
  38c641d1
- Updates in iCLIP, with different mapping params. · 9dd243ee
  Blaise Li authored 4 years ago
  9dd243ee
Jul 31, 2020
- Genome info can be loaded from separate .yaml. · 38df356d
  Blaise Li authored 4 years ago
  
  38df356d
Feb 24, 2020
- Adding licence. · 334fed2c
  Blaise Li authored 5 years ago
  
  334fed2c
- Using extra chromosomes (for transgenes). · d34a6f77
  Blaise Li authored 5 years ago
  d34a6f77
Dec 09, 2019
- Using more processors to map and index. · aaf097a4
  Blaise Li authored 5 years ago
  aaf097a4
Oct 30, 2019
- Trying to use libreads for id conversions. · f6ff4000
  Blaise Li authored 5 years ago
  
  f6ff4000
- Reverting snakefiles to use plain wrappers_dir. · e10a0af2
  Blaise Li authored 5 years ago
  
  e10a0af2
- Fix path to snakemake wrappers. · 0eb879a8
  Blaise Li authored 5 years ago
  
  0eb879a8
Oct 28, 2019
- Packaging snakemake wrappers. · 4d011079
  Blaise Li authored 5 years ago
  
  4d011079
- More requirements specified. Missing dir link. · 30730e63
  Blaise Li authored 5 years ago
  
  30730e63
Oct 14, 2019
- Added ressource used by snakemake wrapper. · b2955080
  Blaise Li authored 5 years ago
  
  b2955080
Apr 16, 2019
- Run from within output_dir. Minor GRO-seq changes. · e4597f9a
  Blaise Li authored 6 years ago
  e4597f9a
Oct 05, 2018
- Summing across a repeat family in shared library. · 304efac1
  Blaise Li authored 6 years ago
  
  304efac1
Oct 04, 2018
- Added --delete option to rsync on success. · 7b21ecbe
  Blaise Li authored 6 years ago
  7b21ecbe
Jun 22, 2018
- Prepare for testing different alignment settings. · 327684d7
  Blaise Li authored 7 years ago
  327684d7
Jun 14, 2018
- Experimenting with alignment settings. · 7a2e276e
  Blaise Li authored 7 years ago
  7a2e276e
Jun 13, 2018
- Fix comma typo in input function (ValueError). · a101b0ce
  Blaise Li authored 7 years ago
  a101b0ce
Jun 08, 2018
- Fix error introduced when fixing normalization. · 182e543a
  Blaise Li authored 7 years ago
  182e543a
- Less stringent remapping parameters. · 4340f14c
  Blaise Li authored 7 years ago
  
  4340f14c
Jun 04, 2018
- Use correct size factor for iCLIP. · 47ac1ab4
  Blaise Li authored 7 years ago
  
  47ac1ab4
Jun 01, 2018
- Remapping unmapped reads for iCLIP. · 00f001de
  Blaise Li authored 7 years ago
  00f001de
Apr 11, 2018
- Upload data even when pipeline fails. · df0bbc29
  Blaise Li authored 7 years ago
  
  df0bbc29
Mar 08, 2018
- Still fixing tex-compatibility, square MA-plots. · afe84326
  Blaise Li authored 7 years ago
  
  afe84326
Mar 05, 2018
- Missing parameter in backup. · 0749173d
  Blaise Li authored 7 years ago
  
  0749173d
Feb 21, 2018
- Cleanup and backup code, factorizing function. · 26aafc43
  Blaise Li authored 7 years ago
  
  26aafc43
Feb 16, 2018
- Fixing extra comma issue (causing tuple of dict). · 4b292bbd
  Blaise Li authored 7 years ago
  
  4b292bbd
Feb 02, 2018
- Pipeline to process iCLIP data. · 53909846
  Blaise Li authored 7 years ago
  53909846