├── .gitattributes ├── .github └── workflows │ ├── CI.yml │ └── Deployment.yml ├── .gitignore ├── .gitmodules ├── Dockerfile ├── LICENSE ├── Makefile ├── Metrics.md ├── README.md ├── THIRD-PARTY-LICENSES.md ├── args.hxx ├── bioio.hpp ├── cloudbuild.yaml ├── python ├── README.md ├── rnaseqc │ ├── __init__.py │ ├── __main__.py │ ├── aggregate.py │ ├── create_notebook.py │ ├── insert_size_intervals.py │ ├── legacy_exon_remap.py │ ├── nb_encode.py │ ├── plot.py │ ├── report.py │ └── run.py └── setup.py ├── src ├── BED.cpp ├── BED.h ├── BamReader.cpp ├── BamReader.h ├── Expression.cpp ├── Expression.h ├── Fasta.cpp ├── Fasta.h ├── GTF.cpp ├── GTF.h ├── Metrics.cpp ├── Metrics.h └── RNASeQC.cpp └── test_data ├── Makefile.linux ├── Makefile.osx ├── approx_diff.py ├── chr1.output ├── chr1.bam.coverage.tsv ├── chr1.bam.exon_reads.gct.gz ├── chr1.bam.gene_fragments.gct.gz ├── chr1.bam.gene_reads.gct.gz ├── chr1.bam.gene_tpm.gct.gz ├── chr1.bam.metrics.tsv ├── chr1.cram.gc_content.tsv └── chr1.cram.metrics.tsv ├── downsampled.bed ├── downsampled.output ├── downsampled.bam.coverage.tsv ├── downsampled.bam.exon_reads.gct.gz ├── downsampled.bam.fragmentSizes.txt ├── downsampled.bam.gene_fragments.gct.gz ├── downsampled.bam.gene_reads.gct.gz ├── downsampled.bam.gene_tpm.gct.gz └── downsampled.bam.metrics.tsv ├── legacy.output ├── downsampled.bam.coverage.tsv ├── downsampled.bam.exon_reads.gct.gz ├── downsampled.bam.fragmentSizes.txt ├── downsampled.bam.gene_fragments.gct.gz ├── downsampled.bam.gene_reads.gct.gz ├── downsampled.bam.gene_tpm.gct.gz ├── downsampled.bam.metrics.tsv ├── legacy.exon_reads.gct.gz └── legacy.gene_reads.gct.gz └── single_pair.output ├── single_pair.bam.exon_reads.gct.gz ├── single_pair.bam.gene_fragments.gct.gz ├── single_pair.bam.gene_reads.gct.gz ├── single_pair.bam.gene_tpm.gct.gz └── single_pair.bam.metrics.tsv /.gitattributes: -------------------------------------------------------------------------------- 1 | -------------------------------------------------------------------------------- /.github/workflows/CI.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/.github/workflows/CI.yml -------------------------------------------------------------------------------- /.github/workflows/Deployment.yml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/.github/workflows/Deployment.yml -------------------------------------------------------------------------------- /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/.gitignore -------------------------------------------------------------------------------- /.gitmodules: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/.gitmodules -------------------------------------------------------------------------------- /Dockerfile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/Dockerfile -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/LICENSE -------------------------------------------------------------------------------- /Makefile: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/Makefile -------------------------------------------------------------------------------- /Metrics.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/Metrics.md -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/README.md -------------------------------------------------------------------------------- /THIRD-PARTY-LICENSES.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/THIRD-PARTY-LICENSES.md -------------------------------------------------------------------------------- /args.hxx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/args.hxx -------------------------------------------------------------------------------- /bioio.hpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/bioio.hpp -------------------------------------------------------------------------------- /cloudbuild.yaml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/cloudbuild.yaml -------------------------------------------------------------------------------- /python/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/README.md -------------------------------------------------------------------------------- /python/rnaseqc/__init__.py: -------------------------------------------------------------------------------- 1 | __version__ = '0.0.3' 2 | -------------------------------------------------------------------------------- /python/rnaseqc/__main__.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/__main__.py -------------------------------------------------------------------------------- /python/rnaseqc/aggregate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/aggregate.py -------------------------------------------------------------------------------- /python/rnaseqc/create_notebook.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/create_notebook.py -------------------------------------------------------------------------------- /python/rnaseqc/insert_size_intervals.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/insert_size_intervals.py -------------------------------------------------------------------------------- /python/rnaseqc/legacy_exon_remap.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/legacy_exon_remap.py -------------------------------------------------------------------------------- /python/rnaseqc/nb_encode.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/nb_encode.py -------------------------------------------------------------------------------- /python/rnaseqc/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/plot.py -------------------------------------------------------------------------------- /python/rnaseqc/report.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/report.py -------------------------------------------------------------------------------- /python/rnaseqc/run.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/rnaseqc/run.py -------------------------------------------------------------------------------- /python/setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/python/setup.py -------------------------------------------------------------------------------- /src/BED.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/BED.cpp -------------------------------------------------------------------------------- /src/BED.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/BED.h -------------------------------------------------------------------------------- /src/BamReader.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/BamReader.cpp -------------------------------------------------------------------------------- /src/BamReader.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/BamReader.h -------------------------------------------------------------------------------- /src/Expression.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/Expression.cpp -------------------------------------------------------------------------------- /src/Expression.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/Expression.h -------------------------------------------------------------------------------- /src/Fasta.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/Fasta.cpp -------------------------------------------------------------------------------- /src/Fasta.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/Fasta.h -------------------------------------------------------------------------------- /src/GTF.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/GTF.cpp -------------------------------------------------------------------------------- /src/GTF.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/GTF.h -------------------------------------------------------------------------------- /src/Metrics.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/Metrics.cpp -------------------------------------------------------------------------------- /src/Metrics.h: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/Metrics.h -------------------------------------------------------------------------------- /src/RNASeQC.cpp: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/src/RNASeQC.cpp -------------------------------------------------------------------------------- /test_data/Makefile.linux: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/Makefile.linux -------------------------------------------------------------------------------- /test_data/Makefile.osx: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/Makefile.osx -------------------------------------------------------------------------------- /test_data/approx_diff.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/approx_diff.py -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.bam.coverage.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.bam.coverage.tsv -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.bam.exon_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.bam.exon_reads.gct.gz -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.bam.gene_fragments.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.bam.gene_fragments.gct.gz -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.bam.gene_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.bam.gene_reads.gct.gz -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.bam.gene_tpm.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.bam.gene_tpm.gct.gz -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.bam.metrics.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.bam.metrics.tsv -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.cram.gc_content.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.cram.gc_content.tsv -------------------------------------------------------------------------------- /test_data/chr1.output/chr1.cram.metrics.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/chr1.output/chr1.cram.metrics.tsv -------------------------------------------------------------------------------- /test_data/downsampled.bed: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.bed -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.coverage.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.coverage.tsv -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.exon_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.exon_reads.gct.gz -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.fragmentSizes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.fragmentSizes.txt -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.gene_fragments.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.gene_fragments.gct.gz -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.gene_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.gene_reads.gct.gz -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.gene_tpm.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.gene_tpm.gct.gz -------------------------------------------------------------------------------- /test_data/downsampled.output/downsampled.bam.metrics.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/downsampled.output/downsampled.bam.metrics.tsv -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.coverage.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.coverage.tsv -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.exon_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.exon_reads.gct.gz -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.fragmentSizes.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.fragmentSizes.txt -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.gene_fragments.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.gene_fragments.gct.gz -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.gene_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.gene_reads.gct.gz -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.gene_tpm.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.gene_tpm.gct.gz -------------------------------------------------------------------------------- /test_data/legacy.output/downsampled.bam.metrics.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/downsampled.bam.metrics.tsv -------------------------------------------------------------------------------- /test_data/legacy.output/legacy.exon_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/legacy.exon_reads.gct.gz -------------------------------------------------------------------------------- /test_data/legacy.output/legacy.gene_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/legacy.output/legacy.gene_reads.gct.gz -------------------------------------------------------------------------------- /test_data/single_pair.output/single_pair.bam.exon_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/single_pair.output/single_pair.bam.exon_reads.gct.gz -------------------------------------------------------------------------------- /test_data/single_pair.output/single_pair.bam.gene_fragments.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/single_pair.output/single_pair.bam.gene_fragments.gct.gz -------------------------------------------------------------------------------- /test_data/single_pair.output/single_pair.bam.gene_reads.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/single_pair.output/single_pair.bam.gene_reads.gct.gz -------------------------------------------------------------------------------- /test_data/single_pair.output/single_pair.bam.gene_tpm.gct.gz: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/single_pair.output/single_pair.bam.gene_tpm.gct.gz -------------------------------------------------------------------------------- /test_data/single_pair.output/single_pair.bam.metrics.tsv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/getzlab/rnaseqc/HEAD/test_data/single_pair.output/single_pair.bam.metrics.tsv --------------------------------------------------------------------------------