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README.Rmd
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---
output: github_document
---
<!-- README.md is generated from README.Rmd. Please edit that file -->
```{r, include = FALSE}
knitr::opts_chunk$set(
collapse = TRUE,
comment = "#>",
fig.path = "man/figures/README-",
out.width = "90%"
)
```
::: {style="margin-top: 5px;"}
<img src="man/figures/hex.jpg" align="right" width="150"/>
:::
## [`sceptre`]{style="font-size:60px;"}
`sceptre` is an R package for single-cell CRISPR screen data analysis, emphasizing statistical rigor, massive scalability, and ease of use.
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[](https://github.com/Katsevich-Lab/sceptre/actions?query=workflow%3AR-CMD-check+branch%3Amain)
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## v0.10.0: `sceptre` at massive scale
`sceptre` v0.10.0 represents another a major upgrade to the `sceptre` software. We have integrated `sceptre` with [`ondisc`](https://timothy-barry.github.io/ondisc/), a companion R package that facilitates large-scale computing on single-cell data. `sceptre` now supports the analysis of single-cell CRISPR screen data out-of-core on a laptop or distributed across hundreds of processors on a computing cluster or cloud.
`sceptre` v0.10.0 includes the following updates:
- Support for disk-backed `sceptre` objects, enabling the analysis of data too large to fit in memory
- A `sceptre` [Nextflow pipeline](https://github.com/timothy-barry/sceptre-pipeline), enabling the deployment of `sceptre` across hundreds of processors on a cluster or cloud
- An updated [e-book](https://timothy-barry.github.io/sceptre-book/) containing new sections about at-scale `sceptre` and the statistical methodology underlying `sceptre`
- New functionality for plotting and inspecting gRNA-to-cell assignments
- A comprehensive suite of unit tests, which verify the correctness of the code
- More detailed man pages (including runnable examples) and minor bug fixes
You can see our [RECOMB poster](https://timothy-barry.github.io/poster_recomb_2024.pdf) for more information about this update.
## Featured publications
- [Barry et al., 2024](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-024-03254-2). "Robust differential expression testing...". *Genome Biology*.
- [Barry et al., 2024](https://timothy-barry.github.io/biostatistics_2024.pdf). "Exponential family measurement error models...". *Biostatistics.*
- [Morris et al., 2023](http://sanjanalab.org/reprints/Morris_Science_2023.pdf). "Discovery of target genes and pathways...". *Science*.
- [Barry et al., 2021](https://genomebiology.biomedcentral.com/articles/10.1186/s13059-021-02545-2). "SCEPTRE improves calibration and sensitivity...". *Genome Biology*.
`sceptre` also recently was featured in a [10x Genomics analysis guide](https://www.10xgenomics.com/analysis-guides/single-cell-crispr-screen-analysis-with-sceptre).
## Bug reports, feature requests, and software questions
For bug reports, please open a [GitHub issue](https://github.com/Katsevich-Lab/sceptre/issues). For questions about `sceptre` functionality, documentation, or how to apply it to your data, please start a discussion under [Q&A](https://github.com/Katsevich-Lab/sceptre/discussions/categories/q-a).