fishash
This is the development version of fishash; to use it, please install the devel version of Bioconductor.
Cell Hashing with One-Sided Fisher Test
Bioconductor version: Development (3.24)
Assigns guide RNAs or other genetic perturbations to cells in single-cell sequencing experiments using a one-sided Fisher's exact test. Implements an iterative refitting procedure to mitigate Simpson's paradox, supports multiple false discovery rate correction methods (Benjamini-Hochberg, Benjamini-Yekutueli, and Guo & Sarkar 2020), and provides simulation utilities for benchmarking demultiplexing methods. Results are returned as SummarizedExperiment objects.
Author: Jack Kamm [aut, cre]
Maintainer: Jack Kamm <jackkamm at gmail.com>
citation("fishash")):Jack Kamm. fishash: Cell Hashing with One-Sided Fisher Test. doi:10.18129/B9.bioc.fishash, R package version 0.99.5, https://bioconductor.org/packages/fishash.
Generated from the package metadata; it may differ from the package's own citation.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("fishash")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("fishash")| Using fishash to assign gRNAs in Perturbseq data | HTML | R Script |
| Reference Manual | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | Preprocessing, Sequencing, SingleCell, Software, StatisticalMethod |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.24 (R-4.6) |
| License | MIT + file LICENSE |
| Depends | R (>= 4.5.0) |
| Imports | dplyr, extraDistr, ggplot2, Matrix, methods, nnet, patchwork, rlang, S4Vectors, SingleCellExperiment, SummarizedExperiment, sparseMatrixStats |
| System Requirements | |
| URL | https://github.com/jackkamm/fishash |
| Bug Reports | https://github.com/jackkamm/fishash/issues |
See More
| Suggests | BiocStyle, ComplexHeatmap, ggExtra, glmGamPoi, knitr, rmarkdown, testthat (>= 3.0.0) |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report, r-universe |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fishash_0.99.5.tar.gz |
| Windows Binary (x86_64) | fishash_0.99.5.zip |
| macOS Binary (big-sur-x86_64) | fishash_0.99.5.tgz |
| macOS Binary (sonoma-arm64) | fishash_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fishash |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fishash |
| Package Short Url | https://bioconductor.org/packages/fishash/ |
| Package Downloads Report | Download Stats |