LICENSE
share/MONSDA/configs/template.json
share/MONSDA/configs/template_base_commented.json
share/MONSDA/configs/template_clean.json
share/MONSDA/configs/tutorial_exhaustive.json
share/MONSDA/configs/tutorial_postprocess.json
share/MONSDA/configs/tutorial_quick.json
share/MONSDA/configs/tutorial_toolmix.json
share/MONSDA/envs/LoveSonesonPatro.yaml
share/MONSDA/envs/base.yaml
share/MONSDA/envs/bbduk.yaml
share/MONSDA/envs/bbmap.yaml
share/MONSDA/envs/bedtools.yaml
share/MONSDA/envs/bwa.yaml
share/MONSDA/envs/bwa2.yaml
share/MONSDA/envs/bwameth.yaml
share/MONSDA/envs/ciri2.yaml
share/MONSDA/envs/countreads.yaml
share/MONSDA/envs/countreads_de.yaml
share/MONSDA/envs/cutadapt.yaml
share/MONSDA/envs/deseq2_DE.yaml
share/MONSDA/envs/dexseq_DEU.yaml
share/MONSDA/envs/dexseq_DTU.yaml
share/MONSDA/envs/diego_DAS.yaml
share/MONSDA/envs/dorado.yaml
share/MONSDA/envs/drimseq_DTU.yaml
share/MONSDA/envs/edger_DAS.yaml
share/MONSDA/envs/edger_DE.yaml
share/MONSDA/envs/edger_DEU.yaml
share/MONSDA/envs/fastp.yaml
share/MONSDA/envs/fastqc.yaml
share/MONSDA/envs/guppy.yaml
share/MONSDA/envs/hisat2.yaml
share/MONSDA/envs/index.yaml
share/MONSDA/envs/isoformswitchanalyzer.yaml
share/MONSDA/envs/kallisto.yaml
share/MONSDA/envs/macs2.yaml
share/MONSDA/envs/macs3.yaml
share/MONSDA/envs/minimap.yaml
share/MONSDA/envs/monsda.yaml
share/MONSDA/envs/monsda_min.yaml
share/MONSDA/envs/multx.yaml
share/MONSDA/envs/peaks.yaml
share/MONSDA/envs/perl.yaml
share/MONSDA/envs/picard.yaml
share/MONSDA/envs/piranha.yaml
share/MONSDA/envs/qc.yaml
share/MONSDA/envs/salmon.yaml
share/MONSDA/envs/samtools.yaml
share/MONSDA/envs/scyphy.yaml
share/MONSDA/envs/segemehl.yaml
share/MONSDA/envs/segemehl3.yaml
share/MONSDA/envs/sra.yaml
share/MONSDA/envs/star.yaml
share/MONSDA/envs/summary.yaml
share/MONSDA/envs/trimgalore.yaml
share/MONSDA/envs/trimm.yaml
share/MONSDA/envs/trimmomatic.yaml
share/MONSDA/envs/trnascan.yaml
share/MONSDA/envs/ucsc.yaml
share/MONSDA/envs/umitools.yaml
share/MONSDA/envs/zip.yaml
share/MONSDA/lib/Collection.groovy
share/MONSDA/profile_nextflow/nextflow.config
share/MONSDA/profile_snakemake/cluster_config.yaml
share/MONSDA/profile_snakemake/config.v8+.yaml
share/MONSDA/profile_snakemake/slurm-jobscript.sh
share/MONSDA/profile_snakemake/slurm-status.py
share/MONSDA/profile_snakemake/slurm-submit-advanced.py
share/MONSDA/profile_snakemake/slurm-submit.py
share/MONSDA/profile_snakemake/slurm_utils.py
share/MONSDA/scripts/Analysis/AddStructure.py
share/MONSDA/scripts/Analysis/CPM_TPM_from_counts.R
share/MONSDA/scripts/Analysis/Cluster2tRNA.py
share/MONSDA/scripts/Analysis/CollectBamStat.py
share/MONSDA/scripts/Analysis/CountEnds.py
share/MONSDA/scripts/Analysis/CountFastqEnds.pl
share/MONSDA/scripts/Analysis/DAS/DIEGO.py
share/MONSDA/scripts/Analysis/DAS/EDGER.R
share/MONSDA/scripts/Analysis/DAS/FeatureCounts2DIEGO.pl
share/MONSDA/scripts/Analysis/DAS/FeatureCounts2DIEGO.py
share/MONSDA/scripts/Analysis/DAS/diego_contrast_files.py
share/MONSDA/scripts/Analysis/DE/DESEQ2.R
share/MONSDA/scripts/Analysis/DE/EDGER.R
share/MONSDA/scripts/Analysis/DE/EDGER_no_rep.R
share/MONSDA/scripts/Analysis/DEU/DEXSEQ.R
share/MONSDA/scripts/Analysis/DEU/EDGER.R
share/MONSDA/scripts/Analysis/DEU/prepare_deu_annotation.py
share/MONSDA/scripts/Analysis/DTU/DEXSEQ.R
share/MONSDA/scripts/Analysis/DTU/DRIMSEQ.R
share/MONSDA/scripts/Analysis/FindPeaks.pl
share/MONSDA/scripts/Analysis/GOA.R
share/MONSDA/scripts/Analysis/GenerateTrackDb.py
share/MONSDA/scripts/Analysis/GettRNAExpression.sh
share/MONSDA/scripts/Analysis/NormalizePeaks.pl
share/MONSDA/scripts/Analysis/PlBed2Bedgraph.pl
share/MONSDA/scripts/Analysis/PreprocessPeaks.pl
share/MONSDA/scripts/Analysis/RemoveSoftClip.py
share/MONSDA/scripts/Analysis/RmdCreator.py
share/MONSDA/scripts/Analysis/SUMMARY/header_summary.Rmd
share/MONSDA/scripts/Analysis/build_DEU_table.py
share/MONSDA/scripts/Analysis/build_DTU_table.py
share/MONSDA/scripts/Analysis/build_count_table.py
share/MONSDA/scripts/Analysis/build_count_table_simple.py
share/MONSDA/scripts/Analysis/build_salmon_table.py
share/MONSDA/scripts/Preprocessing/indexfa.sh
share/MONSDA/scripts/Shells/MergeExpression_Cufflinks.sh
share/MONSDA/scripts/Shells/MergeExpression_RNAcounter.sh
share/MONSDA/scripts/Shells/MergeGeneExpression_Cufflinks.sh
share/MONSDA/scripts/Shells/NonUniqueBam_woPicard.sh
share/MONSDA/scripts/Shells/Sam2Bam.sh
share/MONSDA/scripts/Shells/Sam2Bed.sh
share/MONSDA/scripts/Shells/UniqueBam_woPicard.sh
share/MONSDA/scripts/Shells/UniqueSam_woPicard.sh
share/MONSDA/scripts/Shells/printEnds.sh
share/MONSDA/scripts/Shells/printFQEnds.sh
share/MONSDA/scripts/Universal/AnnotateBed.pl
share/MONSDA/scripts/Universal/Bed2Bedgraph.pl
share/MONSDA/scripts/Universal/ExtendBed.pl
share/MONSDA/scripts/Universal/countCCA.pl
share/MONSDA/scripts/Universal/sam2fastq.pl
share/MONSDA/scripts/lib/Collection.pm
share/MONSDA/scripts/lib/Logger.py
share/MONSDA/scripts/lib/__init.py__
share/MONSDA/scripts/lib/_lib.R
share/MONSDA/workflows/annotatebed.smk
share/MONSDA/workflows/bbduk.nf
share/MONSDA/workflows/bbduk.smk
share/MONSDA/workflows/bwa.nf
share/MONSDA/workflows/bwa.smk
share/MONSDA/workflows/bwa2.nf
share/MONSDA/workflows/bwa2.smk
share/MONSDA/workflows/bwameth.nf
share/MONSDA/workflows/bwameth.smk
share/MONSDA/workflows/ciri2.nf
share/MONSDA/workflows/ciri2.smk
share/MONSDA/workflows/collect.nf
share/MONSDA/workflows/countreads.nf
share/MONSDA/workflows/countreads.smk
share/MONSDA/workflows/cutadapt.nf
share/MONSDA/workflows/cutadapt.smk
share/MONSDA/workflows/deseq2_DE.nf
share/MONSDA/workflows/deseq2_DE.smk
share/MONSDA/workflows/dexseq_DEU.nf
share/MONSDA/workflows/dexseq_DEU.smk
share/MONSDA/workflows/dexseq_DTU.nf
share/MONSDA/workflows/dexseq_DTU.smk
share/MONSDA/workflows/diego_DAS.nf
share/MONSDA/workflows/diego_DAS.smk
share/MONSDA/workflows/dorado.nf
share/MONSDA/workflows/dorado.smk
share/MONSDA/workflows/drimseq_DTU.nf
share/MONSDA/workflows/drimseq_DTU.smk
share/MONSDA/workflows/edger_DAS.nf
share/MONSDA/workflows/edger_DAS.smk
share/MONSDA/workflows/edger_DE.nf
share/MONSDA/workflows/edger_DE.smk
share/MONSDA/workflows/edger_DEU.nf
share/MONSDA/workflows/edger_DEU.smk
share/MONSDA/workflows/fastp.nf
share/MONSDA/workflows/fastp.smk
share/MONSDA/workflows/fastqc.nf
share/MONSDA/workflows/fastqc.smk
share/MONSDA/workflows/fastqc_dedup.nf
share/MONSDA/workflows/fastqc_dedup.smk
share/MONSDA/workflows/fastqc_dedup_trim.nf
share/MONSDA/workflows/fastqc_dedup_trim.smk
share/MONSDA/workflows/fastqc_raw.nf
share/MONSDA/workflows/fastqc_raw.smk
share/MONSDA/workflows/fastqc_trim.nf
share/MONSDA/workflows/fastqc_trim.smk
share/MONSDA/workflows/footer.nf
share/MONSDA/workflows/footer.smk
share/MONSDA/workflows/guppy.nf
share/MONSDA/workflows/guppy.smk
share/MONSDA/workflows/header.nf
share/MONSDA/workflows/header.smk
share/MONSDA/workflows/hisat2.nf
share/MONSDA/workflows/hisat2.smk
share/MONSDA/workflows/kallisto.nf
share/MONSDA/workflows/kallisto.smk
share/MONSDA/workflows/kallisto_trim.smk
share/MONSDA/workflows/macs2.nf
share/MONSDA/workflows/macs2.smk
share/MONSDA/workflows/macs3.nf
share/MONSDA/workflows/macs3.smk
share/MONSDA/workflows/manipulate_genome.nf
share/MONSDA/workflows/manipulate_genome.smk
share/MONSDA/workflows/mapping.nf
share/MONSDA/workflows/mapping.smk
share/MONSDA/workflows/minimap.nf
share/MONSDA/workflows/minimap.smk
share/MONSDA/workflows/multiqc.nf
share/MONSDA/workflows/multiqc.smk
share/MONSDA/workflows/multx.smk
share/MONSDA/workflows/notify.nf
share/MONSDA/workflows/peaks.nf
share/MONSDA/workflows/peaks.smk
share/MONSDA/workflows/picard_dedup.nf
share/MONSDA/workflows/picard_dedup.smk
share/MONSDA/workflows/piranha.nf
share/MONSDA/workflows/piranha.smk
share/MONSDA/workflows/premultiqc.nf
share/MONSDA/workflows/premultiqc.smk
share/MONSDA/workflows/salmon.nf
share/MONSDA/workflows/salmon.smk
share/MONSDA/workflows/salmon_trim.smk
share/MONSDA/workflows/scyphy.nf
share/MONSDA/workflows/scyphy.smk
share/MONSDA/workflows/segemehl.nf
share/MONSDA/workflows/segemehl.smk
share/MONSDA/workflows/segemehl3.nf
share/MONSDA/workflows/segemehl3.smk
share/MONSDA/workflows/segemehl3_bisulfite.nf
share/MONSDA/workflows/segemehl3_bisulfite.smk
share/MONSDA/workflows/segemehl_bisulfite.nf
share/MONSDA/workflows/segemehl_bisulfite.smk
share/MONSDA/workflows/simulatetrim.nf
share/MONSDA/workflows/simulatetrim.smk
share/MONSDA/workflows/sra.nf
share/MONSDA/workflows/sra.smk
share/MONSDA/workflows/star.nf
share/MONSDA/workflows/star.smk
share/MONSDA/workflows/summary.nf
share/MONSDA/workflows/summary.smk
share/MONSDA/workflows/trimgalore.nf
share/MONSDA/workflows/trimgalore.smk
share/MONSDA/workflows/ucsc.nf
share/MONSDA/workflows/ucsc.smk
share/MONSDA/workflows/umitools.nf
share/MONSDA/workflows/umitools.smk
share/MONSDA/workflows/umitools_dedup.nf
share/MONSDA/workflows/unlock.smk
site-packages/MONSDA/Configurator.py
site-packages/MONSDA/Deprecated.py
site-packages/MONSDA/Logger.py
site-packages/MONSDA/Params.py
site-packages/MONSDA/RunMONSDA.py
site-packages/MONSDA/Utils.py
site-packages/MONSDA/Workflows.py
site-packages/MONSDA/__init__.py
site-packages/MONSDA/__main__.py
site-packages/MONSDA/_version.py
site-packages/MONSDA/lib/Collection.groovy
site-packages/MONSDA/web_configurator.py
site-packages/monsda-1.3.0.dist-info/INSTALLER
site-packages/monsda-1.3.0.dist-info/METADATA
site-packages/monsda-1.3.0.dist-info/RECORD
site-packages/monsda-1.3.0.dist-info/REQUESTED
site-packages/monsda-1.3.0.dist-info/WHEEL
site-packages/monsda-1.3.0.dist-info/direct_url.json
site-packages/monsda-1.3.0.dist-info/entry_points.txt
site-packages/monsda-1.3.0.dist-info/licenses/LICENSE
site-packages/monsda-1.3.0.dist-info/top_level.txt
