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("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 | ||
| 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 |