├── .gitignore ├── AUTHORS ├── COPYING ├── INSTALL ├── LICENSE ├── MANUAL ├── README.md ├── TODO ├── galaxy └── ribodiff.xml ├── scripts └── TE.py ├── setup.py ├── src └── ribodiff │ ├── __init__.py │ ├── adjdisp.py │ ├── adjlik.py │ ├── creatematrix.py │ ├── estimatedisp.py │ ├── fitdisp.py │ ├── functional_test_te.py │ ├── loadinput.py │ ├── normalize.py │ ├── parseopts.py │ ├── plot.py │ ├── rawdisp.py │ ├── testcnt.py │ └── writeres.py ├── test-data ├── README ├── experiment_design.csv ├── read_count_table.tab ├── ribodiff_log.txt └── ribodiff_out.tab ├── tests ├── TE_test.py ├── __init__.py ├── experimental_design.csv ├── gene_count_table.tab └── test_gene_count_table.tab └── tools ├── cnt_sim ├── concatenate.py └── nbinom_count_generator.py └── pipeline ├── README.md ├── align_reads ├── align_RF.sh └── align_RNA.sh ├── count_reads └── count_expression.pysam.py ├── filter_reads ├── filtering_RF.py └── filtering_RNA.py └── identify_rRNA ├── align_rRNA.sh ├── generate_rRNA_ref.sh ├── get_rRNA_reads.py └── rRNA_ref_human └── biomart_silva_human_rRNA.fasta /.gitignore: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/.gitignore -------------------------------------------------------------------------------- /AUTHORS: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/AUTHORS -------------------------------------------------------------------------------- /COPYING: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/COPYING -------------------------------------------------------------------------------- /INSTALL: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/INSTALL -------------------------------------------------------------------------------- /LICENSE: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/LICENSE -------------------------------------------------------------------------------- /MANUAL: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/MANUAL -------------------------------------------------------------------------------- /README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/README.md -------------------------------------------------------------------------------- /TODO: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/TODO -------------------------------------------------------------------------------- /galaxy/ribodiff.xml: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/galaxy/ribodiff.xml -------------------------------------------------------------------------------- /scripts/TE.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/scripts/TE.py -------------------------------------------------------------------------------- /setup.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/setup.py -------------------------------------------------------------------------------- /src/ribodiff/__init__.py: -------------------------------------------------------------------------------- 1 | __version__="0.2.1" 2 | -------------------------------------------------------------------------------- /src/ribodiff/adjdisp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/adjdisp.py -------------------------------------------------------------------------------- /src/ribodiff/adjlik.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/adjlik.py -------------------------------------------------------------------------------- /src/ribodiff/creatematrix.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/creatematrix.py -------------------------------------------------------------------------------- /src/ribodiff/estimatedisp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/estimatedisp.py -------------------------------------------------------------------------------- /src/ribodiff/fitdisp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/fitdisp.py -------------------------------------------------------------------------------- /src/ribodiff/functional_test_te.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/functional_test_te.py -------------------------------------------------------------------------------- /src/ribodiff/loadinput.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/loadinput.py -------------------------------------------------------------------------------- /src/ribodiff/normalize.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/normalize.py -------------------------------------------------------------------------------- /src/ribodiff/parseopts.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/parseopts.py -------------------------------------------------------------------------------- /src/ribodiff/plot.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/plot.py -------------------------------------------------------------------------------- /src/ribodiff/rawdisp.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/rawdisp.py -------------------------------------------------------------------------------- /src/ribodiff/testcnt.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/testcnt.py -------------------------------------------------------------------------------- /src/ribodiff/writeres.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/src/ribodiff/writeres.py -------------------------------------------------------------------------------- /test-data/README: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/test-data/README -------------------------------------------------------------------------------- /test-data/experiment_design.csv: -------------------------------------------------------------------------------- 1 | ../tests/experimental_design.csv -------------------------------------------------------------------------------- /test-data/read_count_table.tab: -------------------------------------------------------------------------------- 1 | ../tests/gene_count_table.tab -------------------------------------------------------------------------------- /test-data/ribodiff_log.txt: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/test-data/ribodiff_log.txt -------------------------------------------------------------------------------- /test-data/ribodiff_out.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/test-data/ribodiff_out.tab -------------------------------------------------------------------------------- /tests/TE_test.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tests/TE_test.py -------------------------------------------------------------------------------- /tests/__init__.py: -------------------------------------------------------------------------------- 1 | __version__="0.2.1" 2 | -------------------------------------------------------------------------------- /tests/experimental_design.csv: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tests/experimental_design.csv -------------------------------------------------------------------------------- /tests/gene_count_table.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tests/gene_count_table.tab -------------------------------------------------------------------------------- /tests/test_gene_count_table.tab: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tests/test_gene_count_table.tab -------------------------------------------------------------------------------- /tools/cnt_sim/concatenate.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/cnt_sim/concatenate.py -------------------------------------------------------------------------------- /tools/cnt_sim/nbinom_count_generator.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/cnt_sim/nbinom_count_generator.py -------------------------------------------------------------------------------- /tools/pipeline/README.md: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/README.md -------------------------------------------------------------------------------- /tools/pipeline/align_reads/align_RF.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/align_reads/align_RF.sh -------------------------------------------------------------------------------- /tools/pipeline/align_reads/align_RNA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/align_reads/align_RNA.sh -------------------------------------------------------------------------------- /tools/pipeline/count_reads/count_expression.pysam.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/count_reads/count_expression.pysam.py -------------------------------------------------------------------------------- /tools/pipeline/filter_reads/filtering_RF.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/filter_reads/filtering_RF.py -------------------------------------------------------------------------------- /tools/pipeline/filter_reads/filtering_RNA.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/filter_reads/filtering_RNA.py -------------------------------------------------------------------------------- /tools/pipeline/identify_rRNA/align_rRNA.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/identify_rRNA/align_rRNA.sh -------------------------------------------------------------------------------- /tools/pipeline/identify_rRNA/generate_rRNA_ref.sh: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/identify_rRNA/generate_rRNA_ref.sh -------------------------------------------------------------------------------- /tools/pipeline/identify_rRNA/get_rRNA_reads.py: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/identify_rRNA/get_rRNA_reads.py -------------------------------------------------------------------------------- /tools/pipeline/identify_rRNA/rRNA_ref_human/biomart_silva_human_rRNA.fasta: -------------------------------------------------------------------------------- https://raw.githubusercontent.com/ratschlab/RiboDiff/HEAD/tools/pipeline/identify_rRNA/rRNA_ref_human/biomart_silva_human_rRNA.fasta --------------------------------------------------------------------------------