Novartis/pisces issues and pull requests

#39 - Fingerprint SNP positions should be hg38 coordinates, not GRCh37

Issue - State: open - Opened by mdshw5 4 months ago

#38 - Update pisces_dependencies command

Pull Request - State: closed - Opened by mdshw5 4 months ago

#37 - Update documentation build and expression summary details

Pull Request - State: closed - Opened by mdshw5 4 months ago

#36 - Update develop

Pull Request - State: closed - Opened by mdshw5 5 months ago

#35 - Exit codes for pisces commands should be nonzero on errors

Issue - State: open - Opened by mdshw5 7 months ago

#34 - Indexing RefSeq transcriptome failure

Issue - State: closed - Opened by mdshw5 12 months ago - 1 comment
Labels: bug

#33 - Update GTF tag handling

Pull Request - State: closed - Opened by mdshw5 about 1 year ago

#32 - Merge changes from master

Pull Request - State: closed - Opened by mdshw5 over 1 year ago

#31 - Update list of problematic protein_coding genes to exclude during --scale-tpm

Issue - State: open - Opened by mdshw5 almost 2 years ago

#30 - Feature: Automatically determine sample type using gene expression

Issue - State: open - Opened by mdshw5 about 2 years ago
Labels: enhancement

#29 - Add dockerfile and ignore development files

Pull Request - State: closed - Opened by mdshw5 over 2 years ago

#28 - Fix the genotyping process to work with gzipped input files

Pull Request - State: closed - Opened by mdshw5 over 2 years ago
Labels: bug

#27 - Add DeprecationWarning for pisces summarize-qc tables

Issue - State: open - Opened by mdshw5 over 2 years ago
Labels: enhancement

#26 - Add user defined GTF tag names, default disable_infer_features

Pull Request - State: closed - Opened by mdshw5 almost 3 years ago

#25 - Don't drop dimensions for matrices with only one sample (#24)

Pull Request - State: closed - Opened by mdshw5 almost 3 years ago

#24 - pisces summarize-expression fails with only one sample

Issue - State: closed - Opened by mdshw5 almost 3 years ago
Labels: bug

#23 - Fix gene-level lengths output

Pull Request - State: closed - Opened by mdshw5 about 3 years ago

#22 - Add gene-level effective lengths (#6)

Pull Request - State: closed - Opened by mdshw5 about 3 years ago

#21 - Fixes auto sample naming

Pull Request - State: closed - Opened by ucpete about 3 years ago - 1 comment

#20 - Bring in recent changes and bug fixes before a new release

Pull Request - State: closed - Opened by mdshw5 about 3 years ago

#19 - Fix the default "auto" sample naming

Issue - State: closed - Opened by mdshw5 about 3 years ago - 5 comments

#18 - Add gene description to annotation matrix

Issue - State: open - Opened by mdshw5 about 3 years ago - 1 comment
Labels: enhancement

#17 - Fix exon ordering for minus strand transcripts in #15

Pull Request - State: closed - Opened by mdshw5 about 3 years ago

#16 - Add "tidy" data output as an option

Issue - State: open - Opened by mdshw5 over 3 years ago
Labels: enhancement

#15 - Reverse order of - strand exons

Issue - State: closed - Opened by mdshw5 over 3 years ago
Labels: bug

#14 - Negate filtering for failing.quartile.filter during deseq.dataset construction

Pull Request - State: closed - Opened by mdshw5 over 3 years ago

#13 - Fix filtering heuristics for low counts data

Issue - State: closed - Opened by mdshw5 over 3 years ago
Labels: bug

#12 - Separate package installation from R/binary dependency management

Pull Request - State: closed - Opened by mdshw5 over 3 years ago

#11 - pip wheels break pisces post-install process

Issue - State: closed - Opened by mdshw5 over 3 years ago
Labels: bug

#10 - remove .DS_Store files

Pull Request - State: closed - Opened by dbrrt over 3 years ago - 1 comment

#9 - Add ERCC spike-in sequences to the default index files

Issue - State: closed - Opened by mdshw5 over 3 years ago
Labels: enhancement

#8 - Add ERCC spike-in FASTA to default salmon index files

Issue - State: closed - Opened by mdshw5 over 3 years ago

#7 - Support for differential transcript expression

Issue - State: open - Opened by mdshw5 over 3 years ago
Labels: enhancement

#6 - Annotate output matrices with salmon effective length

Issue - State: closed - Opened by mdshw5 over 3 years ago - 2 comments
Labels: enhancement

#5 - QC metrics we need to aggregate

Issue - State: open - Opened by mdshw5 almost 4 years ago
Labels: enhancement

#4 - Detect binaries automatically if they are in the PATH

Issue - State: open - Opened by guma44 almost 4 years ago - 1 comment
Labels: enhancement

#3 - Use salmon's automatic --libtype detection

Issue - State: closed - Opened by mdshw5 almost 4 years ago
Labels: enhancement

#2 - pisces dependencies command fails

Issue - State: closed - Opened by mdshw5 almost 4 years ago - 2 comments
Labels: bug

#1 - Build Docker images with pre-installed PISCES

Issue - State: open - Opened by mdshw5 almost 4 years ago - 1 comment

GitHub / Novartis/pisces issues and pull requests