RNASeq: Add gene body coverage plots to multiqc report. Restore ability to opt out of contamination checking via tools_off. Properly invoke threading for verifybamid2. Fix circular import issue when using bcbio functions outside of the main bcbio script. Enable setting custom PureCN options via YAML file
Split out assertive imports so we can pin on bioconda. Improved package documentation. Improve dlabe...
Updates bcbio.rnaseq to use transcript level counts from Sailfish, using Mike Love's tximport librar...
Provide initial support for nanopore RNA-seq data (cDNA/direct RNA). See README for example usage fo...
Update ChIP and ATAC bowtie2 runs to use --very-sensitive. Properly pad TSS BED file for ataqv TSS e...
Import shared dependency functions from bcbioBase instead of basejump. Added method support for sele...
1.2.5 (01 January 2021) Joint calling for RNA-seq variant calling requires setting jointcaller to b...
Simplified dependencies to make it installable with bioconda. Added clusterProfiler with functions t...
Fix vcf header bug: T/N SAMPLE lines are back - needed for import to SolveBio add strandedness: auto...
Preparing for installation via bioconda Adds a --version flag for post-installation sanity checking
Fix for get VEP cache. Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY)...
RNASeq: Fail more gracefully if SummarizedExperiment object cannot be created. Fixes to handle DRAGE...
Adds initial support for Sleuth and handling of bcbio-nextgen runs where Qualimap rnaseq could not r...
1.2.4 (21 September 2020) Remove deprecated --genomicsdb-use-vcf-codec option as this is now the de...
Fix for bismark not being a supported aligner. Run ataqv (https://github.com/ParkerLab/ataqv) to cal...
stabled object containing bcbio RNAseq output Code compatible with best practices and BioC rules Rep...
Split out assertive imports so we can pin on bioconda. Improved package documentation. Improve dlabe...
Updates bcbio.rnaseq to use transcript level counts from Sailfish, using Mike Love's tximport librar...
Provide initial support for nanopore RNA-seq data (cDNA/direct RNA). See README for example usage fo...
Update ChIP and ATAC bowtie2 runs to use --very-sensitive. Properly pad TSS BED file for ataqv TSS e...
Import shared dependency functions from bcbioBase instead of basejump. Added method support for sele...
1.2.5 (01 January 2021) Joint calling for RNA-seq variant calling requires setting jointcaller to b...
Simplified dependencies to make it installable with bioconda. Added clusterProfiler with functions t...
Fix vcf header bug: T/N SAMPLE lines are back - needed for import to SolveBio add strandedness: auto...
Preparing for installation via bioconda Adds a --version flag for post-installation sanity checking
Fix for get VEP cache. Support Picard's new syntax for ReorderSam (REFERENCE -> SEQUENCE_DICTIONARY)...
RNASeq: Fail more gracefully if SummarizedExperiment object cannot be created. Fixes to handle DRAGE...
Adds initial support for Sleuth and handling of bcbio-nextgen runs where Qualimap rnaseq could not r...
1.2.4 (21 September 2020) Remove deprecated --genomicsdb-use-vcf-codec option as this is now the de...
Fix for bismark not being a supported aligner. Run ataqv (https://github.com/ParkerLab/ataqv) to cal...
stabled object containing bcbio RNAseq output Code compatible with best practices and BioC rules Rep...
Split out assertive imports so we can pin on bioconda. Improved package documentation. Improve dlabe...
Updates bcbio.rnaseq to use transcript level counts from Sailfish, using Mike Love's tximport librar...
Provide initial support for nanopore RNA-seq data (cDNA/direct RNA). See README for example usage fo...