Reg Gen Versions Save

Regulatory Genomics Toolbox: Python library and set of tools for the integrative analysis of high throughput regulatory genomics data.

0.11.5

5 years ago

RGT

  • updated the genomic data link in SetupGenomicData.py

HINT

  • improved differential footprinting analysis
  • fixed expectation problem

0.11.4

5 years ago

RGT

  • #79: the RGTDATA environment variable should now be correctly handled both when installing and at runtime

  • fixed Zebrafish chromosome names

MotifAnalysis

  • fixed a bug that prevented the reverse strand from being checked

  • added a few unit tests

  • fixed mtf files

HINT

  • improved normalisation

TDF

  • fixed typo

0.11.3

6 years ago
  • HINT: improved the differential analysis of footprints, now a scatter plot will be output where the factors that pass a Gaussian-based test will be highlighted.

0.11.2

6 years ago

  • Motif Analysis: upgraded Hocomoco to v11 and Jaspar Vertebrates to v7 (2018). Also changed a bit the options (see help and tutorial on the website for details) and added the possibility to pass, via command line, a custom motif repository via the --motif-db option; it must be a directory made of .pwm files, just like the default repositories.

  • THOR: fixed a bug when calculating GC content (introduced in the previous release)

0.11.1

6 years ago

  • HINT: big refactoring for the paper version, check out the tutorial.

  • Motif Analysis: massively improved performance (100x speed) and also made it more verbose (#41)

  • TDF: several small bug fixes

0.10.2

6 years ago
  • Fixed random seed setting in THOR

0.10.1

6 years ago

  • Randomisation is now more controlled - with seeds

  • Closed a few THOR bugs

  • MacOS support should now be OK

  • Pysam dependency upgraded to 0.12.X

  • Removed Biopython dependency from Motif Analysis tool

0.10.0

6 years ago

  • HINT: optimised HMM model and bias correction method for ATAC-seq

  • THOR: fixed #25

  • Improved MacOS support

  • Does not support hmmlearn 0.1.1

0.9.9

7 years ago
  • HINT: fixed bias correction error
  • THOR: fixed report paths (#22) and temporary files lingering
  • rgt-core: fixed CoverageSet that also left temporary files around

0.9.8

7 years ago
  • Fixed environmental markers in dependency (broken with <2016 python versions)
  • THOR: fixed matplotlib and numpy warnings, plus added a sort command after bigWigMerge command
  • Motif analysis: made sure all paths are normalised (eg, ~ is now correctly expanded)
  • fixed import issue with RGT-Viz