scTree

scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data - Published in JOSS (2020)

https://github.com/jspaezp/sctree

Scientific Fields

Repository

Tree based marker finding and gating visualization for single cell rna seq data

README.Rmd

---
title: "sctree: a package to connect single cell rna-seq to biology using trees"
output: 
  github_document:
    toc: true
    toc_depth: 2
---



```{r setup, include = FALSE}
knitr::opts_chunk$set(
  collapse = TRUE,
  comment = "#>"
)

knitr::opts_chunk$set(
  fig.path = "man/figures/"
)
```

[![Travis build status](https://travis-ci.org/jspaezp/sctree.svg?branch=master)](https://travis-ci.org/jspaezp/sctree)
[![Coverage status](https://codecov.io/gh/jspaezp/sctree/branch/master/graph/badge.svg)](https://codecov.io/github/jspaezp/sctree?branch=master)
[![status](https://joss.theoj.org/papers/4316d75e1e458003f7acfee08fd3922b/status.svg)](https://joss.theoj.org/papers/4316d75e1e458003f7acfee08fd3922b)

# sctree

The goal of scTree is to provide allow biologists to identify a minimal set
of genes from single-cell RNA-seq (scRNA-seq) data that can be used in downstream
experiments. While there are already methods available to identify differentially
expressed genes and markers that differ between subpopulations in scRNA-seqdata,
there are generally too many genes in these lists to use in follow-up experiments.

Features suggesting pseudo-gating strategies to purify found populations
via flow-cytometry, antibody querying and cross validations between
datasets.

Please check our companion documentation website hosted at
[jspaezp.github.io/sctree](https://jspaezp.github.io/sctree/).

Number of lines in roxygen comments:
`r system2("bash", "-c \"grep -RP '^#' ./R | wc -l\"", stdout = TRUE)`

Number of lines in R code:
`r system2("bash", "-c \"grep -RP '^[^#]' ./R | grep -vP '^$' | wc -l \"", stdout = TRUE)`


```{r child="vignettes/rmdchunks/_installation.Rmd"}
```

```{r child="vignettes/rmdchunks/_usage_intro.Rmd"}
```

```{r child="vignettes/rmdchunks/_finding_markers.Rmd"}
```

```{r child="vignettes/rmdchunks/_visualizing_markers.Rmd"}
```

```{r child="vignettes/rmdchunks/_suggesting_strategies.Rmd"}
```

```{r child="vignettes/rmdchunks/_antibodies.Rmd"}
```

```{r}
sessionInfo()
```


# Steps down the road

3. Address some of the TODO's in this repository
4. Reduce dependecies by replacing functions to base equivalents.
5. Add links to the documentation to make nicer to explore the package from inside R
8. Implement a way to find markers for clusters exclusively upregulated
9. Refctor the code to make the coding nomenclature same as seurat

Owner

JOSS Publication

scTree: An R package to generate antibody-compatible classifiers from single-cell sequencing data

Published

April 26, 2020

DOI

10.21105/joss.02061

Volume 5, Issue 48, Page 2061

Authors

J. Sebastian Paez
Purdue University, Center for Cancer Research, Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology

Michael K. Wendt
Purdue University, Center for Cancer Research, Purdue University, Department of Medicinal Chemistry and Molecular Pharmacology

Nadia Atallah Lanman
Purdue University, Center for Cancer Research, Purdue University, Department of Comparative Pathobiology

Editor

Will Rowe

Tags

Bioinformatics Single cell Flow Cytometry

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