External tools and applications
- scRNA-Seq
- scVelo: RNA Velocity generalized through dynamical modeling
- SoupX: R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data
- DropletUtils: Clone of the Bioconductor repository for the DropletUtils package
- signac: R toolkit for the analysis of single-cell chromatin data
- SnapATAC: Analysis Pipeline for Single Cell ATAC-seq
- Scrublet: Detect doublets in single-cell RNA-seq data
- cellHarmony: RNA Velocity generalized through dynamical modeling
- DoubletDecon: A tool for removing doublets from single-cell RNA-seq data
- Scanpy: Single-Cell Analysis in Python
- Seurat: R toolkit for single cell genomics
- Monocle3: An analysis toolkit for single-cell RNA-Seq experiments.
- SLICE: Determining Cell Differentiation and Lineage based on Single Cell Entropy
- BackSPIN: scRNA-seq analysis: cell type identification (biclustering)
- Celloline / Cellity: Mapping and quality assessment scRNA-seq data
- ICGS: Unsupervised Single-Cell Expression Profile Identification
- Monocle: extracting lineage relationships from scRNA-seq and modeling the dynamic changes associated with cell differentiation
- RaceID: Single cell cell type identification (rare and abundant cell types)
- SCDE: The scde package implements a set of statistical methods for analyzing single-cell RNA-seq data
- scLVM: clustering, confounding factor analysis
- SCUBA: cell ordering, lineage tree reconstruction, bifurcation analysis
- Sincera: Single cell RNA-seq analysis to identify: cell types, cell type specific gene signatures; and driving forces of given cell types.
- Singular: scRNA-seq analysis: clustering, cell type identification, cell outlier detection
- SNN-Cliq: scRNA-seq analysis: clustering, cell type identification
- Wanderlust: scRNA-seq analysis: cell ordering
- NGS
- AltAnalyze : Free Software Package (Gene expression and alternative splicing analyses on microarrays, RNASeq data and single cell data.)
- BamTools: BamTools provides both a programmer's API and an end-user's toolkit for handling BAM files.
- Biowardrobe: ChIP-Seq and RNA-Seq data
- BRB-ArrayTools: Free Software Package (Microarray gene expression, copy number, methylation and RNA-Seq data)
- DEGseq: R package, DE analysis
- DESeq: R package, sequencing assays and DE analysis
- EdgeR: R package, DE analysis
- FastQC: NGS data Quality control
- Galaxy: Galaxy is an open source, web-based platform for data intensive biomedical research.
- Genomatix: Commercial Software Suite( TF DB, NGS data analysis, Genomic data mining)
- NOISeq: R package, QA/QC,differential expression (DE) analysis
- Partek: Commercial Software Suite (alignment, RNA-Seq, small RNA-Seq, DNA-Seq, and ChIP-Seq).
- Qualimap 2: QA/QC, counts output
- Qualimap 2: http://www.bioconductor.org/help/workflows/rnaseqGene/
- SAMtools: SAM (Sequence Alignment/Map) is a flexible generic format for storing nucleotide sequence alignment. SAMtools provide efficient utilities on manipulating alignments in the SAM format.
- StrandNGS: Commercial Software Suite (alignment, RNA-Seq, small RNA-Seq, DNA-Seq, Methyl-Seq, MeDIP-Seq, and ChIP-Seq)
- Metacore: Omics data mining
- Clustering
- Enrichment Analysis
- Graphics and visualization tool
- Other