Updated citation for snakePipes Fixed replicate check for samples with trailing spaces in names Fixed input filtering in CSAW Several allele-specific RNAseq fixes ATACseq peakQC is now run on fragment-size filtered bam Fixed Salmon output (Number of Reads output in "*counts.tsv" files and file naming) Fixed CSAW QC plot error with single end reads Updated histone HMM environment to a working conda version Salmon_wasabi is now a localrul
RNAseq workflow is now called mRNA-seq added noncoding-RNA-seq workflow added STARsolo mode to scRNA...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
Fixed a bug in the ATAC-seq environment where GenomeInfoDbData was missing. Also an occasional issue...
snakePipes 2.2.0 Added Alevin mode in scRNA workflow Added a new conda environment using to call Al...
Bug fixes: multiQC in RNAseq allelic checks for successful sample identification in workflows where...
snakePipes 2.2.3 Genrich will now run if sampleSheet without replicates is provided. Updated zenodo...
Snakemake version is bumped to 5.13.0 Updated docs on running single snakefiles Added user-input tar...
snakePipes 2.4.2 Deeptools coverage RPKM in mRNA-seq and noncoding-RNA-seq worflows now respects bl...
A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were ...
snakePipes 2.4.3 Fixed noncoding-RNA-seq workflow without sample sheet. Updated links to prebuilt i...
snakePipes 2.3.0 Deprecated mode Gruen in scRNAseq. scRNAseq mode Alevin now outputs spliced/unspli...
snakePipes 2.2.1 Fix a bug in DAG for ChIPseq allelic with CSAW. Fixed deepTools qc DAG for ChIPseq...
snakePipes 2.3.1 Fixed aligner options for bwa in DNA-mapping. Fixed allelic mode for single end re...
snakePipes 2.4.0 Added support for multiple pairwise comparisons for DESeq2, sleuth, and rMats in t...
The initial production release, supporting RNA-seq, ChIP-seq, scRNA-seq (Cel-seq2), ATAC-seq and mor...
RNAseq workflow is now called mRNA-seq added noncoding-RNA-seq workflow added STARsolo mode to scRNA...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
Fixed a bug in the ATAC-seq environment where GenomeInfoDbData was missing. Also an occasional issue...
snakePipes 2.2.0 Added Alevin mode in scRNA workflow Added a new conda environment using to call Al...
Bug fixes: multiQC in RNAseq allelic checks for successful sample identification in workflows where...
snakePipes 2.2.3 Genrich will now run if sampleSheet without replicates is provided. Updated zenodo...
Snakemake version is bumped to 5.13.0 Updated docs on running single snakefiles Added user-input tar...
snakePipes 2.4.2 Deeptools coverage RPKM in mRNA-seq and noncoding-RNA-seq worflows now respects bl...
A wide number of bug fixes to scRNA-seq and other pipelines. In particular, many memory limits were ...
snakePipes 2.4.3 Fixed noncoding-RNA-seq workflow without sample sheet. Updated links to prebuilt i...
snakePipes 2.3.0 Deprecated mode Gruen in scRNAseq. scRNAseq mode Alevin now outputs spliced/unspli...
snakePipes 2.2.1 Fix a bug in DAG for ChIPseq allelic with CSAW. Fixed deepTools qc DAG for ChIPseq...
snakePipes 2.3.1 Fixed aligner options for bwa in DNA-mapping. Fixed allelic mode for single end re...
snakePipes 2.4.0 Added support for multiple pairwise comparisons for DESeq2, sleuth, and rMats in t...
The initial production release, supporting RNA-seq, ChIP-seq, scRNA-seq (Cel-seq2), ATAC-seq and mor...
RNAseq workflow is now called mRNA-seq added noncoding-RNA-seq workflow added STARsolo mode to scRNA...
snakePipes 2.2.2 Fix DAG inconsistencies for ChIP-seq and ATAC-seq ran fromBAM and from -d. DESeq2 ...
Fixed a bug in the ATAC-seq environment where GenomeInfoDbData was missing. Also an occasional issue...