scfind

This package is for version 3.9 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: 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 (!require("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")
`scfind` package vignette HTML R Script
Reference Manual PDF
NEWS Text

Details

biocViews DataRepresentation, GeneExpression, ImmunoOncology, RNASeq, Sequencing, SingleCell, Software, Transcription, Transcriptomics
Version 1.6.0
In Bioconductor since BioC 3.6 (R-3.4) (6.5 years)
License GPL-3
Depends R (>= 3.4)
Imports SingleCellExperiment, SummarizedExperiment, methods, stats, bit, dplyr, hash, reshape2, Rcpp (>= 0.12.12)
System Requirements
URL https://github.com/hemberg-lab/scfind
Bug Reports https://support.bioconductor.org/t/scfind/
See More
Suggests knitr, rmarkdown, testthat
Linking To Rcpp
Enhances
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report Build Report

Package Archives

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

Source Package scfind_1.6.0.tar.gz
Windows Binary scfind_1.6.0.zip (32- & 64-bit)
Mac OS X 10.11 (El Capitan) scfind_1.6.0.tgz
Source Repository git clone https://git.bioconductor.org/packages/scfind
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/scfind
Bioc Package Browser https://code.bioconductor.org/browse/scfind/
Package Short Url https://bioconductor.org/packages/scfind/
Package Downloads Report Download Stats
Old Source Packages for BioC 3.9 Source Archive