Frequently Asked Questions

Single-sample Gene Set Enrichment Analysis (ssGSEA) calculates separate enrichment scores for each paring of a sample and gene set. Enrichment scores represent the degree to which the genes in a particular gene set are coordinately up or down regulated within a sample.

Identify somatic short variants (SNVs and Indels) in one or more tumor samples from a single individual, with or without a matched normal sample.

TEtranscripts and TEcount takes RNA-seq (and similar data) and annotates reads to both genes & transposable elements. TEtranscripts then performs differential analysis using DESeq2.

Map annotations between assemblies of the same, or closely-related species.

This Gatk4 pipeline is intended for calling variants in samples that are clonal – i.e. a single individual.

Perform differential intron retention analysis on RNA-sequencing data using DESeq2.

Performs Gene Set Enrichment Analysis on a ranked list of genes (ex. the output of DESeq2 or LimmaVoom)

The tRNA-Seq Pipeline automates tRNA expression and modification analysis. It clusters tRNAs, handles modifications, aligns reads, calculates coverage, quantifies expression, detects differential expression, and analyzes tRNA functionality and modifications.

Nfcore/atacseq is a bioinformatics analysis pipeline used for ATAC-seq data.

scRNA-Analysis-Module is a pipeline that analyzes single cell RNA-Seq data. It takes in one or more h5 file and do doublet-removal, filtering, normalization, batch effect correction, dimension reduction and clustering.

nf-core/proteinfold is a bioinformatics best-practice analysis pipeline for Protein 3D structure prediction pipeline.

This is a "Stork" pipeline for Via Foundry's powerful scViewer shiny App: the input for this pipeline is Seurat object in .rds file. This pipeline helps researchers who want to bring their own Seurat analysis results and visualize them using scViewer.

nfcore/ampliseq is a bioinformatics analysis pipeline used for amplicon sequencing, supporting denoising of any amplicon and supports a variety of taxonomic databases for taxonomic assignment including 16S, ITS, CO1 and 18S.

Quantifies gene/feature counts from BAM inputs. Optionally runs differential expression analysis using DESeq2 or Limma Voom.

This Gatk4 pipeline is intended for calling variants in samples that are clonal – i.e. a single individual.

This is a Spatial Transcriptome Analysis pipeline based on spatialdata and scanpy. The input is '.tar' compressed (not '.tar.gz'!) folder(s) from Xenium output. The output is one html file per sample regarding QC and clustering and one .zarr.tar file per sample. If there are more than one sample, an aggregated html report will be generated.

Identify somatic short variants (SNVs and Indels) in a matched tumor and normal sample.

Nfcore/chipseq is a bioinformatics analysis pipeline used for Chromatin ImmunopreciPitation sequencing (ChIP-seq) data.