README.Rmd

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

<!-- README.md is generated from README.Rmd. Please edit that file -->

```{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