Package: fishash 0.99.3

Jack Kamm

fishash: Cell Hashing with One-Sided Fisher Test

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.

Authors:Jack Kamm [aut, cre]

fishash_0.99.3.tar.gz
fishash_0.99.3.zip(r-4.7-any)fishash_0.99.3.zip(r-4.6-any)fishash_0.99.3.zip(r-4.5-any)
fishash_0.99.3.tgz(r-4.6-any)fishash_0.99.3.tgz(r-4.5-any)
fishash_0.99.3.tar.gz(r-4.7-any)fishash_0.99.3.tar.gz(r-4.6-any)
fishash_0.99.3.tgz(r-4.6-emscripten)
manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
fishash/json (API)

# Install 'fishash' in R:

install.packages('fishash', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/jackkamm/fishash/issues

Datasets:

tapseq_diffex - TAPseq benchmark dataset

On BioConductor:fishash-0.99.3(bioc 3.24)

singlecell sequencing preprocessing statisticalmethod

5.44 score 5 stars 10 scripts 7 exports 48 dependencies

Last updated from:2454c9575d. Checks:1 NOTE, 9 OK. Indexed: yes.

Target	Result	Time
bioc-checks	NOTE	207
linux-devel	OK	378
source / vignettes	OK	436
linux-release	OK	319
macos-release	OK	270
macos-oldrel	OK	157
windows-devel	OK	241
windows-release	OK	259
windows-oldrel	OK	216
wasm-release	OK	152

Exports:diagonal_heatmap fishash impute_masked_counts nonzero_histogram_with_weighted simulate_guidebender simulate_guidebender2 sort_columns_by_top_row

Dependencies:abind Biobase BiocGenerics cli cpp11 DelayedArray dplyr extraDistr farver generics GenomicRanges ggplot2 glue gtable IRanges isoband labeling lattice lifecycle magrittr Matrix MatrixGenerics matrixStats nnet patchwork pillar pkgconfig R6 RColorBrewer Rcpp RcppArmadillo rlang S4Arrays S4Vectors S7 scales Seqinfo SingleCellExperiment SparseArray sparseMatrixStats SummarizedExperiment tibble tidyselect utf8 vctrs viridisLite withr XVector

Using fishash to assign gRNAs in Perturbseq data

Rendered fromfishash-vignette.Rmdusingknitr::rmarkdown

Last update: 2026-07-26
Started: 2026-01-23

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Plot guide count matrix as an approximately diagonal heatmap	diagonal_heatmap
Cell hashing by one-sided Fisher test	fishash
For a matrix of counts, impute masked entries via an alternating algorithm	impute_masked_counts
Plot histogram and weighted histogram of UMI counts	nonzero_histogram_with_weighted
Simulate guide count matrix based on a cellbender-like model	simulate_guidebender
Alternative interface to 'simulate_guidebender' that tries to have more interpretable input parameters, in particular: Signal to Noise Ratio, count per cell, and fraction of noise that is endogeneous vs exogeneous. These replace the following parameters from 'simulate_guidebender' which should not be used with this function: 'd_mu_drop', 'd_mu_cell', 'rho_alpha', 'rho_beta'.	simulate_guidebender2
Sort matrix columns to place maxes near diagonal	sort_columns_by_top_row
TAPseq benchmark dataset (Schraivogel et al 2020)	tapseq_diffex