RGT-0.11.5

RGT

• updated the genomic data link in SetupGenomicData.py

HINT

• improved differential footprinting analysis
• fixed expectation problem

RGT-0.11.4

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

RGT-0.11.3

• 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.

RGT-0.11.2

• 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)

RGT-0.11.1

• 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

RGT-0.10.2

• Fixed random seed setting in THOR

RGT-0.10.1

• 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

RGT-0.10.0

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

• THOR: fixed #25

• Improved MacOS support

• Does not support hmmlearn 0.1.1

RGT-0.9.9

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

RGT-0.9.8

• 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