scfind

DOI: 10.18129/B9.bioc.scfind    

This package is for version 3.11 of Bioconductor. This package has been removed from Bioconductor. For the last stable, up-to-date release version, see scfind.

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

Bioconductor version: Release (3.11)

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>

Installation

To install this package, start R (version "4.0") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("scfind")

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, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics
Version	1.9.0
In Bioconductor since	BioC 3.6 (R-3.4) (3 years)
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_1.9.0.tar.gz
Windows Binary	scfind_1.9.0.zip (32- & 64-bit)
macOS 10.13 (High Sierra)
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	https://bioconductor.org/packages/scfind/
Package Downloads Report	Download Stats