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")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
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 | 0.99.3 |
| 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 |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | fishash_0.99.3.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | fishash_0.99.3.tgz |
| macOS Binary (sonoma-arm64) | fishash_0.99.3.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/fishash |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/fishash |
| Bioc Package Browser | https://code.bioconductor.org/browse/fishash/ |
| Package Short Url | https://bioconductor.org/packages/fishash/ |
| Package Downloads Report | Download Stats |