seandavi / awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
MIT License
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analysis analysis-pipeline atac-seq awesome-list bioinformatics cell-clusters cell-cycle cell-differentiation cell-populations clustering data-integration data-visualization dimensionality-reduction gene-expression gene-expression-profiles python rna-seq-data rna-seq-experiments scrna-seq-data single-cell

awesome-single-cell

List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Contributions welcome...

Citation

DOI

Contents

Software packages

RNA-seq

Quality control

Gene regulatory network identification

Immune receptor profiling

Marker and differential gene expression identification

Cell clustering

Dimension reduction

Archetypal analysis

Count modelling and normalization

Batch-effect removal

Cell projection and unimodal integration

Simulation

Pseudotime and trajectory inference

Cell type identification and classification

Doublet Identification

Cell subsampling

Feature (Gene) imputation

Copy number analysis

Variant calling

Epigenomics

Multi-assay data integration

Rare cell detection

Cellular interactions/communication

Single cell large model

Other applications

Spatial transcriptomics

Tutorials and workflows

Web portals, apps, and databases

Web portals and databases

Interactive visualization and analysis

Journal articles of general interest

Paper collections

Big data approach overview

Experimental design

Methods comparisons

Similar lists and collections

People

Gender bias at conferences is a well known problem (http://www.sciencemag.org/careers/2015/07/countering-gender-bias-conferences). Creating a list of potential speakers can help mitigate this bias and a community of people developing and maintaining helps to further diversify this list beyond smaller networks.

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