Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.
List of software packages (and the people developing these methods) for single-cell data analysis, including RNA-seq, ATAC-seq, etc. Contributions welcome...
HTSeq
is htseq-count
, a script to quantify gene expression in bulk and single-cell RNA-Seq and similar experiments.kb-python
is a python package for processing single-cell RNA-sequencing. It wraps the kallisto
| bustools
single-cell RNA-seq command line tools in order to unify multiple processing workflows.cellassign
automatically assigns single-cell RNA-seq data to known cell types across thousands of cells accounting for patient and batch specific effects. Information about a priori known markers for cell types is provided as input to the model. cellassign then probabilistically assigns each cell to a cell type, removing subjective biases from typical unsupervised clustering workflows. bioRxiv
inferCNV
. Significantly faster than the R version.gget
is a free, open-source command-line tool and Python package that enables efficient querying of genomic databases. gget
consists of a collection of separate but interoperable modules, each designed to facilitate one type of database querying in a single line of code.tsv
download. Over 500 single cell transcriptomics studies have been published to date. Many of these have data available, but the links between data, study, and systems studied can be hard to identify through literature search. This manuscript describes a nearly exhaustive and manually curated database of single cell transcriptomics studies with descriptions of what kind of data and what biological systems have been studied. bioRxiv.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.