v4.0.7

What's Changed - these were already part of 4.0.6 tagged version.

• Bug Fix in integrateBatches.R URD call by @wong-nw in #449
• Improved QC Reports - June 2020 (NW) by @wong-nw in #451
• ChIP-seq improvements by @tovahmarkowitz in #460
• scRNA QC and integration fixes by @wong-nw in #463
• Fixing reference to /scratch in novocraft sort rule in activeDev by @mtandon09 in #466
• Fixing reference to /scratch in novocraft sort rule by @mtandon09 in #465
• (master branch) Run freec only for hg38 and hg19 by @mtandon09 in #468
• Run freec only for hg38 and hg19 by @mtandon09 in #467
• ChIP-seq pipeline improvements by @tovahmarkowitz in #472
• Merge activeDev 4.0.6 into master by @slsevilla in #483

What's changed: these were NOT part of 4.0.6 merge

• ChIP-seq updates: estimated fragment length and more by @tovahmarkowitz in #450

Full Changelog: v4.0.2...v4.0.7

Release v4.0.2

v4.0.2

Release Notes:

• Default python version changing to 3.7: 85ba637
• Updated STAR cmd to increase mapping rate: fa67a91
• New differential expression entry point from counts matrix: de9ab35
• Sequenza error fix: 2c1b1a3
• Addition of miDeep2-based miR-seq pipeline: 27c045b
• Latest single-cell RNA-seq updates: 27c045b
• Removed AVIA: 63a5ce9
• Updated git version in submission script: 749f808

Major updates on RNA-seq and ChIP-seq Pipelines

This is the release of Pipeliner on July 2017.
There are updates on RNA-seq pipeline and ChIP-seq Pipeline.

Release on 2017/02/17

Merge pull request #202 from jlac/master

added full path to genome output files to fix avia bug

btep201702

Release for the BTEP class