The following websites provide software and tools for bioinformatics analysis.

  • Subread: a general-purpose read aligner which can align both genomic DNA-seq and RNA-seq reads.
  • Bowtie2: is an ultrafast and memory-efficient tool for aligning sequencing reads to long
    reference sequences.
  • featureCounts: a ultrafast and accurate read summarization program.
  • edgeR: differential analysis of sequence read count data.
  • GSEA: A knowledge-based approach for interpreting genome-wide expression profiles.
  • Metascape: A Gene Annotation & Analysis Resource.
  • Enrichr: a comprehensive gene set enrichment analysis web server.
  • TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.
  • GREAT: predicts functions of cis-regulatory regions.
  • ChIP-Atlas: An integrative, comprehensive database to explore public Epigenetic dataset.
  • miRDeep2: is a software package for identification of novel and known miRNAs in deep sequencing data.
  • QIIME 2™: is a next-generation microbiome bioinformatics platform that is extensible, free, open source, and community developed.
  • BS-Seeker2: a versatile aligning pipeline for bisulfite sequencing data.
  • CGmapTools: support BS-seq data analyses with command-lines.
  • Cell Ranger: Cell Ranger is a set of analysis pipelines that process Chromium single cell data to align reads, generate feature-barcode matrices, perform clustering and other secondary analysis.
  • Loupe Browser: Loupe Browser is a desktop application that provides interactive visualization functionality to analyze data from different 10x Genomics solutions. Loupe Browser allows you to easily interrogate different views of your 10x Genomics data to quickly gain insights into the underlying biology.
  • Seurat: Seurat is an R package designed for QC, analysis, and exploration of single-cell RNA-seq data. Seurat aims to enable users to identify and interpret sources of heterogeneityfrom single-cell transcriptomic measurements, and to integrate diverse types of single-cell data.
  • Signac: Signac is designed for the analysis of single-cell chromatin data, including scATAC-seq, single-cell targeted tagmentation methods such as scCUT&Tag and scNTT-seq, and multimodal datasets that jointly measure chromatin state alongside other modalities.
  • Harmony: Harmony is a general-purpose R package with an efficient algorithm for integrating multiple data sets. It is especially useful for large single-cell datasets such as single-cell RNA-seq.
  • Monocle 3: The Monocle 3 package provides a toolkit for analyzing single-cell gene expression experiments, including clustering, classifying, and counting cells, constructing single-cell trajectories, differential expression analysis.
  • SingleR: Performs unbiased cell type recognition from single-cell RNA sequencing data, by leveraging reference transcriptomic datasets of pure cell types to infer the cell of origin of each single cell independently.
  • CellMarker: CellMarker provides a user-friendly interface for browsing, searching and downloading markers of diverse cell types of different tissues. Furthermore, a summarized marker prevalence in each cell type is graphically and intuitively presented through a vivid statistical graph.
  • ArchR: ArchR is a full-featured R package for processing and analyzing single-cell ATAC-seq data. ArchR provides the most extensive suite of scATAC-seq analysis tools of any software available.
  • SnapATAC: SnapATAC is a comprehensive bioinformatic solution for single-cell ATAC-seq analysis.
  • SPARK: is a R package developed to identify genes with spatial expression pattern in spatially resolved transcriptomic studies.
  • CARDfree: is a reference-based deconvolution method used for estimating the cell type composition in spatial transcriptomics data. This approach relies on cell type-specific expression information obtained from a reference single-cell RNA sequencing (scRNA-seq) dataset.
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