Processes by category

Atac-seq

• ATAC-Seq

Align

• BWA MEM2

• Bowtie (Dicty)

• Bowtie2

• HISAT2

• BWA MEM

• BWA SW

• BWA ALN

• STAR

Bam processing

• Bam split

• Bedtools bamtobed

• Calculate coverage (bamCoverage)

• Bamplot

• Bamliquidator

• Annotate novel splice junctions (regtools)

• Bamclipper

• MarkDuplicates

• alignmentSieve

Chip-seq

• MACS 1.4

• Pre-peakcall QC

• ChIP-Seq (Peak Score)

• ChIP-Seq (Gene Score)

• ChIP-seq (MACS2)

• ChIP-seq (MACS2-ROSE2)

• ROSE2

• MACS 2.0

• ChipQC

Differential expression

• edgeR

• Cuffdiff 2.2

• DESeq2

• Differential expression of shRNA

Enrichment and clustering

• PCA

• Find similar genes

• Hierarchical clustering of time courses

Fastq processing

• UMI-tools dedup

• Subsample FASTQ (single-end)

• Subsample FASTQ (paired-end)

• Merge FASTQ (single-end)

• Merge FASTQ (paired-end)

• Reverse complement FASTQ (single-end)

• Reverse complement FASTQ (paired-end)

• Cutadapt (single-end)

• Cutadapt (paired-end)

• Trimmomatic (single-end)

• Trimmomatic (paired-end)

• Trim Galore (paired-end)

• Cutadapt (3’ mRNA-seq, single-end)

• Cutadapt (Corall RNA-Seq, single-end)

• Cutadapt (Corall RNA-Seq, paired-end)

• BBDuk (single-end)

• BBDuk (paired-end)

Gatk

• GATK SelectVariants (multi-sample)

• GATK SelectVariants (single-sample)

• GATK VariantFiltration (multi-sample)

• GATK VariantFiltration (single-sample)

• GATK GenomicsDBImport

• GATK4 (HaplotypeCaller)

• GATK filter variants (VQSR)

• GATK HaplotypeCaller (GVCF)

• GATK MergeVcfs

• GATK GenotypeGVCFs

• GATK VariantsToTable

• GATK refine variants

• BaseQualityScoreRecalibrator

• RNA-seq variant calling preprocess

• GATK SplitNCigarReads

Genome index

• Bowtie2 genome index

• BWA genome index

• Bowtie genome index

• BWA-MEM2 genome index

• HISAT2 genome index

• STAR genome index

Import

• GEO import

• Upload microarray expression (unmapped)

• VCF file

• GAF file

• GFF3 file

• GTF file

• SAM header

• OBO file

• Mappability info

• Cuffquant results

• Reads (QSEQ multiplexed, single)

• Reads (QSEQ multiplexed, paired)

• Differential Expression (table)

• BED file

• BAM file

• BAM file and index

• Secondary hybrid BAM file

• Expression time course

• IDAT file

• ML-ready expression

• Ensembl-VEP cache directory

• BaseSpace file

• Metadata table (one-to-one)

• Metadata table

• FASTQ file (single-end)

• FASTQ file (paired-end)

• Convert files to reads (single-end)

• Convert files to reads (paired-end)

• Gene set

• Gene set (create)

• Gene set (create from Venn diagram)

• BEDPE file

• SRA data

• SRA data (single-end)

• SRA data (paired-end)

• Upload proteomics sample

• Upload proteomics sample set

• Reads (scRNA 10x)

• BWA-MEM2 index files

• Single cell BAM file and index

• FASTA file

Other

• Prepare GEO - ChIP-Seq

• Prepare GEO - RNA-Seq

• Convert GFF3 to GTF

• Archive samples

Picard

• Picard AlignmentSummary

• Picard CollectRrbsMetrics

• Picard InsertSizeMetrics

• Picard WGS Metrics

Pipeline

• Cut & Run

• WGBS (single-end)

• WGBS (paired-end)

• miRNA pipeline

• RNA-Seq (Cuffquant)

• Cutadapt - STAR - StringTie (Corall, single-end)

• Cutadapt - STAR - StringTie (Corall, paired-end)

• WGS (paired-end) analysis

• Whole exome sequencing (WES) analysis

• shRNA quantification

• Chemical Mutagenesis

• MACS2 - ROSE2

• MACS2

• Subsample FASTQ and BWA Aln (single-end)

• Subsample FASTQ and BWA Aln (paired-end)

• STAR-based gene quantification workflow

• BBDuk - Salmon - QC

• BBDuk - STAR - featureCounts - QC

• Beta Cut & Run workflow

• RNA-seq Variant Calling Workflow

• QuantSeq workflow

• WGS analysis (GVCF)

Qc

• Spike-ins quality control

• QoRTs QC

• MultiQC

• RNA-SeQC

Quantify

• Detect library strandedness

• Merge Expressions (ETC)

• Quantify shRNA species using bowtie2

• Cuffnorm

• Expression aggregator

• Expression matrix

• Cufflinks 2.2

• Dictyostelium expressions

• Salmon Index

• Cuffquant 2.2

• Mappability

• Expression Time Course

• Cuffmerge

Samtools

• Samtools idxstats

• Samtools view

• Samtools coverage (multi-sample)

• Samtools coverage (single-sample)

• Samtools bedcov

• Samtools fastq (paired-end)

Test

• Abstract alignment process

• Abstract expression process

• Abstract differential expression process

• Test basic fields

• Test sleep progress

• Test hidden inputs

• Test disabled inputs

• Test select controler

• Abstract annotation process

• Abstract bed process

Vep

• Ensembl Variant Effect Predictor

Wgbs

• HMR

• methcounts

• WALT

• WALT genome index

• Bisulfite conversion rate

Wgs

• Variant calling (CheMut)

• Variant filtering (CheMut)

• snpEff (General variant annotation) (multi-sample)

• snpEff (General variant annotation) (single-sample)

• WGS preprocess data with bwa-mem2

Xenograft processing

• Xengsort index

• Xengsort classify

Scrna-seq

• Cell Ranger Mkref

• Cell Ranger Count

Uncategorized

• Map microarray probes