Index

A

Abstract alignment process Abstract annotation process Abstract bed process Abstract differential expression process Abstract expression process Accel Amplicon Pipeline Align (BWA) and trim adapters alignmentSieve Alleyoop collapse

Alleyoop rates Alleyoop snpeval Alleyoop summary Alleyoop UTR Rates Amplicon report Amplicon table Annotate novel splice junctions (regtools) Archive and make multi-sample report for amplicon data Archive samples ATAC-Seq

B

BAM file BAM file and index Bam split Bamclipper Bamliquidator Bamplot BaseQualityScoreRecalibrator BaseSpace file BBDuk (paired-end) (single-end) BBDuk - Salmon - QC (paired-end) (single-end) BBDuk - STAR - FeatureCounts (3' mRNA-Seq, paired-end) (3' mRNA-Seq, single-end) BBDuk - STAR - featureCounts - QC (paired-end) (single-end)

BBDuk - STAR - HTSeq-count (paired-end) (single-end) BED file BEDPE file Bedtools bamtobed BioProcessTestCase (class in resolwe_bio.utils.test) Bisulfite conversion rate Bowtie (Dicty) Bowtie genome index Bowtie2 Bowtie2 genome index BWA ALN BWA genome index BWA MEM BWA SW

C

Cell Ranger Count Cell Ranger Mkref Chemical Mutagenesis ChIP-Seq (Gene Score) ChIP-seq (MACS2) (MACS2-ROSE2) ChIP-Seq (Peak Score) ChipQC Convert files to reads (paired-end) (single-end) Convert GFF3 to GTF coverageBed Cuffdiff 2.2 Cufflinks 2.2 Cuffmerge Cuffnorm Cuffquant 2.2

Cuffquant results Custom master file Cut & Run Cutadapt (3' mRNA-seq, single-end) (Corall RNA-Seq, paired-end) (Corall RNA-Seq, single-end) (Diagenode CATS, paired-end) (Diagenode CATS, single-end) (paired-end) (single-end) Cutadapt - STAR - FeatureCounts (3' mRNA-Seq, single-end) Cutadapt - STAR - FeatureCounts - basic QC (3' mRNA-Seq, single-end) Cutadapt - STAR - HTSeq-count (paired-end) (single-end) Cutadapt - STAR - RSEM (Diagenode CATS, paired-end) (Diagenode CATS, single-end) Cutadapt - STAR - StringTie (Corall, paired-end) (Corall, single-end)

D

Deeptools bamCoverage DESeq2 Detect library strandedness

Dictyostelium expressions Differential Expression (table) Differential expression of shRNA

E

edgeR Expression aggregator Expression data (Cuffnorm) (STAR)

Expression matrix Expression Time Course Expression time course

F

FASTA file FASTQ file (paired-end) (single-end)

featureCounts Find similar genes

G

GAF file GATK3 (HaplotypeCaller) GATK4 (HaplotypeCaller) Gene expression indices Gene set (create from Venn diagram) (create)

GEO import GFF3 file GO Enrichment analysis GTF file

H

Hierarchical clustering of genes Hierarchical clustering of samples Hierarchical clustering of time courses HISAT2

HISAT2 genome index HMR HTSeq-count (CPM) (TPM)

I

Indel Realignment and Base Recalibration

K

KBBioProcessTestCase (class in resolwe_bio.utils.test)

L

LoFreq (call)

M

MACS 1.4 MACS 2.0 MACS2 MACS2 - ROSE2 Mappability Mappability info MarkDuplicates Merge Expressions (ETC)

Merge FASTQ (paired-end) (single-end) Metadata table for Orange methcounts miRNA pipeline module resolwe_bio.utils resolwe_bio.utils.test MultiQC

O

OBO file

P

PCA Picard AlignmentSummary Picard CollectRrbsMetrics Picard CollectTargetedPcrMetrics Picard InsertSizeMetrics Picard WGS Metrics Pre-peakcall QC Prepare GEO - ChIP-Seq

Prepare GEO - RNA-Seq prepare_amplicon_master_file() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_annotation() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_annotation_gff() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_bam() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_expression() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_paired_reads() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_reads() (resolwe_bio.utils.test.BioProcessTestCase method) prepare_ref_seq() (resolwe_bio.utils.test.BioProcessTestCase method)

Q

QoRTs QC

Quantify shRNA species using bowtie2

R

Reads (QSEQ multiplexed, paired) (QSEQ multiplexed, single) (scRNA 10x) resolwe_bio.utils module resolwe_bio.utils.test module

Reverse complement FASTQ (paired-end) (single-end) RNA-Seq (Cuffquant) ROSE2 RSEM

S

Salmon Index Salmon Quant SAM header Samtools idxstats Secondary hybrid BAM file setUp() (resolwe_bio.utils.test.BioProcessTestCase method) (resolwe_bio.utils.test.KBBioProcessTestCase method) shRNA quantification Single cell BAM file and index skipDockerFailure() (in module resolwe_bio.utils.test) skipUnlessLargeFiles() (in module resolwe_bio.utils.test) Slam count

Slamdunk (paired-end) snpEff, [1] Spike-ins quality control SRA data (paired-end) (single-end) STAR STAR genome index Subsample FASTQ (paired-end) (single-end) Subsample FASTQ and BWA Aln (paired-end) (single-end)

T

Test basic fields Test disabled inputs Test hidden inputs Test select controler Test sleep progress

Trim Galore (paired-end) Trimmomatic (paired-end) (single-end) Trimmomatic - HISAT2 - HTSeq-count (paired-end) (single-end)

U

UMI-tools dedup Upload Picard CollectTargetedPcrMetrics

Upload proteomics sample Upload proteomics sample set

V

Variant calling (CheMut)

Variant filtering (CheMut) VCF file

W

WALT WALT genome index WGBS (paired-end) (single-end)

WGS (paired-end) analysis Whole exome sequencing (WES) analysis Whole length Slamdunk analysis (paired-end) Writing processes