scfind

DOI: 10.18129/B9.bioc.scfind    

This is the development version of scfind; for the stable release version, see scfind.

A search tool for single cell RNA-seq data by gene lists

Bioconductor version: Development (3.9)

Recently a very large collection of single-cell RNA-seq (scRNA-seq) datasets has been generated and publicly released. For the collection to be useful, the information must be organized in a way that supports queries that are relevant to researchers. `scfind` builds an index from scRNA-seq datasets which organizes the information in a suitable and compact manner so that the datasets can be very efficiently searched for either cells or cell types in which a given list of genes is expressed.

Author: Vladimir Kiselev

Maintainer: Vladimir Kiselev <vladimir.yu.kiselev at gmail.com>

Citation (from within R, enter citation("scfind")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("scfind", version = "3.9")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("scfind")

 

HTML R Script `scfind` package vignette
PDF   Reference Manual
Text   NEWS

Details

biocViews DataRepresentation, GeneExpression, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics
Version 1.5.0
License GPL-3
Depends R (>= 3.4)
Imports SingleCellExperiment, SummarizedExperiment, methods, stats, bit, dplyr, hash, reshape2, Rcpp (>= 0.12.12)
LinkingTo Rcpp
Suggests knitr, rmarkdown, testthat
SystemRequirements
Enhances
URL https://github.com/hemberg-lab/scfind
BugReports https://support.bioconductor.org/t/scfind/
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package scfind_1.5.0.tar.gz
Windows Binary scfind_1.5.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scfind_1.5.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scfind
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scfind
Package Short Url http://bioconductor.org/packages/scfind/
Package Downloads Report Download Stats

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