RGT-1.0.2

RGT

• Now supports the M1 chip for MacOS both with arm64 and x86_64 (#253 )

RGT-1.0.0

RGT

• Now supports the M1 chip for MacOS
• Add more reference genome

HINT

• Fixed a bug of wrongly removing overlapping regions for predicted motif binding sites

Motif analysis

• Script setupLogoData.py now uses the logomaker package to generate logos

RGT-viz

• More examples are added

RGT-0.13.2

RGT

• genomes aligned with Gencode "reference" : mouse 25 and human 21

HINT

• fixed NAN problem when the number of TFBSs is low

Motif Analysis

• #178: added Jaspar Insects

RGT-0.13.1

RGT Core

• #154 gene annotation is no longer divided between genes_Gencode and genes_RefSeq, but uses a single key gene_regions. Users that have modified their data.config.user must change it accordingly.

HINT

• added smooth function to differential analysis
• used built-in function from pysam to calculate the number of reads

Viz

• removed argument warn from matlibplot.use function

Motif Analysis

• #155 minor changes to output

RGT-0.13.0

RGT

• #12 upgraded to Python 3.6+. Python 2 is no longer supported

Motif Analysis

• #139 updated JASPAR motif database
• #102 temporarily removed gProfiler link in enrichment output
• #117 default to no warning for duplicate gene names

THOR

• #124 fixed p-value representation in output files

RGT-0.12.3

HINT

• #131 Included PyX with specific version 0.12.1, manual installation is no longer needed.

RGT-0.12.2

HINT

• #126 Removed weblogo3 dependency due to a connection error.
• Differential footprinting analysis now supports three or more conditions.

RGT-0.12.1

RGT

• Minor release change - possible compatibility break with previous versions
• #107 MOODS no longer requires a manual installation step
• Travis now runs unit tests on Mac OS too, to ensure support of the platform
• Library versions and minor python 3 compatibility changes applied

Motif Analysis

• #111 Many changes in the handling of custom motif repositories (documented here)
• Added a filter parameter, to further subset the chosen motif databases
• Increased unit test coverage
• Some scripts, previously only internal, are now copied to the $RGTDATA/motifs folder

HINT

• Added a function to check the presence of index files
• HINT now will only use the mapped reads for footprinting and differential analysis

RGT-0.11.7

TDF

• New feature for autobinding is added.
• Feature for running Triplexes is modified.

RGT-0.11.6

RGT

• pyBigWig==0.3.12, because the version later doesn't support py27.
• links in setupGenomoicDate.py are updated.

TDF

• Help messages are updated.
• Normalization TTS counts is implemented.
• Many minor issues are fixed.