Processes by category¶
Differential expression¶
Import¶
- GAF file
- VCF file
- Genome
- Expression data
- Expression data (Cuffnorm)
- Expression data (STAR)
- SAM header
- Upload Picard CollectTargetedPcrMetrics
- Metabolic pathway file
- BAM file
- BAM file and index
- Secondary hybrid BAM file
- Cuffquant results
- BED file
- SRA data
- SRA data (single-end)
- SRA data (paired-end)
- FASTA file
- BaseSpace file
- Differential Expression (table)
- OBO file
- Custom master file
- GFF3 file
- GTF file
- Mappability info
- Reads (QSEQ multiplexed, single)
- Reads (QSEQ multiplexed, paired)
- snpEff
- 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)
- Expression time course
Other¶
- Amplicon report
- Archive and make multi-sample report for amplicon data
- PCA
- Hierarchical clustering of samples
- Hierarchical clustering of genes
- Bam split
- Prepare GEO - ChIP-Seq
- Prepare GEO - RNA-Seq
- MultiQC
- Convert GFF3 to GTF
- Archive samples
- Spike-ins quality control
- Subsample FASTQ (single-end)
- Subsample FASTQ (paired-end)
- ChIP-Seq (Peak Score)
- ChIP-Seq (Gene Score)
- Cutadapt (Diagenode CATS, single-end)
- Cutadapt (Diagenode CATS, paired-end)
- GO Enrichment analysis
- STAR genome index
- coverageBed
- Bamliquidator
- Align (BWA) and trim adapters
- Picard CollectTargetedPcrMetrics
- Amplicon table
- Merge Expressions (ETC)
- Mappability
- Expression matrix
- Gene expression indices
- Expression aggregator
- Dictyostelium expressions
- Expression Time Course
- Indel Realignment and Base Recalibration
- Variant filtering (CheMut)
- Variant calling (CheMut)
- GATK3 (HaplotypeCaller)
- GATK4 (HaplotypeCaller)
- snpEff
- LoFreq (call)
Pipeline¶
- ATAC-Seq
- BBDuk - STAR - HTSeq-count (single-end)
- BBDuk - STAR - HTSeq-count (paired-end)
- WGBS
- Cutadapt - STAR - RSEM (Diagenode CATS, single-end)
- Cutadapt - STAR - RSEM (Diagenode CATS, paired-end)
- BBDuk - Salmon - QC (single-end)
- BBDuk - Salmon - QC (paired-end)
- Cutadapt - STAR - StringTie (Corall, single-end)
- Cutadapt - STAR - StringTie (Corall, paired-end)
- BBDuk - STAR - featureCounts - QC (single-end)
- BBDuk - STAR - featureCounts - QC (paired-end)
- RNA-Seq (Cuffquant)
- BBDuk - STAR - FeatureCounts (3’ mRNA-Seq, single-end)
- BBDuk - STAR - FeatureCounts (3’ mRNA-Seq, paired-end)
- Cutadapt - STAR - HTSeq-count (single-end)
- Cutadapt - STAR - HTSeq-count (paired-end)
- Chemical Mutagenesis
- Slamdunk analysis (paired-end)
- Accel Amplicon Pipeline
- shRNA quantification
- Whole exome sequencing (WES) analysis
- Trimmomatic - HISAT2 - HTSeq-count (single-end)
- Trimmomatic - HISAT2 - HTSeq-count (paired-end)
- MACS2 - ROSE2
- miRNA pipeline
- Cutadapt - STAR - FeatureCounts (3’ mRNA-Seq, single-end)
- Cutadapt - STAR - FeatureCounts - basic QC (3’ mRNA-Seq, single-end)