LICENSE
MANIFEST.in
README.md
pyproject.toml
setup.cfg
setup.py
versioneer.py
MONSDA/Configurator.py
MONSDA/Deprecated.py
MONSDA/Logger.py
MONSDA/Params.py
MONSDA/RunMONSDA.py
MONSDA/Utils.py
MONSDA/Workflows.py
MONSDA/__init__.py
MONSDA/__main__.py
MONSDA/_version.py
MONSDA.egg-info/PKG-INFO
MONSDA.egg-info/SOURCES.txt
MONSDA.egg-info/dependency_links.txt
MONSDA.egg-info/entry_points.txt
MONSDA.egg-info/not-zip-safe
MONSDA.egg-info/requires.txt
MONSDA.egg-info/top_level.txt
MONSDA/lib/Collection.groovy
configs/template.json
configs/template_base_commented.json
configs/template_clean.json
configs/tutorial_exhaustive.json
configs/tutorial_postprocess.json
configs/tutorial_quick.json
configs/tutorial_toolmix.json
envs/LoveSonesonPatro.yaml
envs/base.yaml
envs/bbduk.yaml
envs/bbmap.yaml
envs/bedtools.yaml
envs/bwa.yaml
envs/bwa2.yaml
envs/bwameth.yaml
envs/ciri2.yaml
envs/countreads.yaml
envs/countreads_de.yaml
envs/cutadapt.yaml
envs/deseq2_DE.yaml
envs/dexseq_DEU.yaml
envs/dexseq_DTU.yaml
envs/diego_DAS.yaml
envs/dorado.yaml
envs/drimseq_DTU.yaml
envs/edger_DAS.yaml
envs/edger_DE.yaml
envs/edger_DEU.yaml
envs/fastqc.yaml
envs/guppy.yaml
envs/hisat2.yaml
envs/index.yaml
envs/isoformswitchanalyzer.yaml
envs/macs.yaml
envs/minimap.yaml
envs/monsda.yaml
envs/peaks.yaml
envs/perl.yaml
envs/picard.yaml
envs/piranha.yaml
envs/qc.yaml
envs/salmon.yaml
envs/samtools.yaml
envs/scyphy.yaml
envs/segemehl.yaml
envs/segemehl3.yaml
envs/sra.yaml
envs/star.yaml
envs/summary.yaml
envs/trimgalore.yaml
envs/trimm.yaml
envs/trimmomatic.yaml
envs/trnascan.yaml
envs/ucsc.yaml
envs/umitools.yaml
envs/zip.yaml
profile_nextflow/nextflow.config
profile_snakemake/cluster_config.yaml
profile_snakemake/config.yaml
profile_snakemake/slurm-jobscript.sh
profile_snakemake/slurm-status.py
profile_snakemake/slurm-submit-advanced.py
profile_snakemake/slurm-submit.py
profile_snakemake/slurm_utils.py
scripts/Analysis/AddStructure.py
scripts/Analysis/Cluster2tRNA.py
scripts/Analysis/CollectBamStat.py
scripts/Analysis/CountEnds.py
scripts/Analysis/CountFastqEnds.pl
scripts/Analysis/FindPeaks.pl
scripts/Analysis/GOA.R
scripts/Analysis/GenerateTrackDb.py
scripts/Analysis/GettRNAExpression.sh
scripts/Analysis/NormalizePeaks.pl
scripts/Analysis/PlBed2Bedgraph.pl
scripts/Analysis/PreprocessPeaks.pl
scripts/Analysis/RemoveSoftClip.py
scripts/Analysis/RmdCreator.py
scripts/Analysis/build_DEU_table.py
scripts/Analysis/build_DTU_table.py
scripts/Analysis/build_count_table.py
scripts/Analysis/build_salmon_table.py
scripts/Analysis/DAS/DIEGO.py
scripts/Analysis/DAS/EDGER.R
scripts/Analysis/DAS/FeatureCounts2DIEGO.pl
scripts/Analysis/DAS/FeatureCounts2DIEGO.py
scripts/Analysis/DAS/diego_contrast_files.py
scripts/Analysis/DE/DESEQ2.R
scripts/Analysis/DE/EDGER.R
scripts/Analysis/DEU/DEXSEQ.R
scripts/Analysis/DEU/EDGER.R
scripts/Analysis/DEU/prepare_deu_annotation.py
scripts/Analysis/DTU/DEXSEQ.R
scripts/Analysis/DTU/DRIMSEQ.R
scripts/Analysis/SUMMARY/header_summary.Rmd
scripts/Preprocessing/indexfa.sh
scripts/Shells/MergeExpression_Cufflinks.sh
scripts/Shells/MergeExpression_RNAcounter.sh
scripts/Shells/MergeGeneExpression_Cufflinks.sh
scripts/Shells/NonUniqueBam_woPicard.sh
scripts/Shells/NonUniqueBam_woPicard.sh~
scripts/Shells/Sam2Bam.sh
scripts/Shells/Sam2Bed.sh
scripts/Shells/UniqueBam_woPicard.sh
scripts/Shells/UniqueBam_woPicard.sh~
scripts/Shells/UniqueSam_woPicard.sh
scripts/Shells/printEnds.sh
scripts/Shells/printFQEnds.sh
scripts/Universal/AnnotateBed.pl
scripts/Universal/Bed2Bedgraph.pl
scripts/Universal/ExtendBed.pl
scripts/Universal/countCCA.pl
scripts/Universal/sam2fastq.pl
scripts/lib/Collection.pm
scripts/lib/Logger.py
scripts/lib/__init.py__
scripts/lib/_lib.R
tests/test_functions.py
workflows/annotatebed.smk
workflows/bbduk.nf
workflows/bbduk.smk
workflows/bwa.nf
workflows/bwa.smk
workflows/bwa2.nf
workflows/bwa2.smk
workflows/bwameth.nf
workflows/bwameth.smk
workflows/ciri2.nf
workflows/ciri2.smk
workflows/collect.nf
workflows/countreads.nf
workflows/countreads.smk
workflows/cutadapt.nf
workflows/cutadapt.smk
workflows/deseq2_DE.nf
workflows/deseq2_DE.smk
workflows/dexseq_DEU.nf
workflows/dexseq_DEU.smk
workflows/dexseq_DTU.nf
workflows/dexseq_DTU.smk
workflows/diego_DAS.nf
workflows/diego_DAS.smk
workflows/dorado.nf
workflows/dorado.smk
workflows/drimseq_DTU.nf
workflows/drimseq_DTU.smk
workflows/edger_DAS.nf
workflows/edger_DAS.smk
workflows/edger_DE.nf
workflows/edger_DE.smk
workflows/edger_DEU.nf
workflows/edger_DEU.smk
workflows/fastqc.nf
workflows/fastqc.smk
workflows/fastqc_dedup.nf
workflows/fastqc_dedup.smk
workflows/fastqc_dedup_trim.nf
workflows/fastqc_dedup_trim.smk
workflows/fastqc_raw.nf
workflows/fastqc_raw.smk
workflows/fastqc_trim.nf
workflows/fastqc_trim.smk
workflows/footer.nf
workflows/footer.smk
workflows/guppy.nf
workflows/guppy.smk
workflows/header.nf
workflows/header.smk
workflows/hisat2.nf
workflows/hisat2.smk
workflows/macs.nf
workflows/macs.smk
workflows/manipulate_genome.nf
workflows/manipulate_genome.smk
workflows/mapping.nf
workflows/mapping.smk
workflows/minimap.nf
workflows/minimap.smk
workflows/multiqc.nf
workflows/multiqc.smk
workflows/notify.nf
workflows/peaks.nf
workflows/peaks.smk
workflows/picard_dedup.nf
workflows/picard_dedup.smk
workflows/piranha.nf
workflows/piranha.smk
workflows/premultiqc.nf
workflows/premultiqc.smk
workflows/salmon.nf
workflows/salmon.smk
workflows/salmon_trim.smk
workflows/scyphy.nf
workflows/scyphy.smk
workflows/segemehl.nf
workflows/segemehl.smk
workflows/segemehl3.nf
workflows/segemehl3.smk
workflows/segemehl3_bisulfite.nf
workflows/segemehl3_bisulfite.smk
workflows/segemehl_bisulfite.nf
workflows/segemehl_bisulfite.smk
workflows/simulatetrim.nf
workflows/simulatetrim.smk
workflows/sra.nf
workflows/sra.smk
workflows/star.nf
workflows/star.smk
workflows/summary.nf
workflows/summary.smk
workflows/trimgalore.nf
workflows/trimgalore.smk
workflows/ucsc.nf
workflows/ucsc.smk
workflows/umitools.nf
workflows/umitools.smk
workflows/umitools_dedup.nf
workflows/unlock.smk