README.Rmd

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output: github_document
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knitr::opts_chunk$set(
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# DPLabR

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The goal of DPLabR is to collect custom functions written in different .R files in different
projects in the same place. The need came up when I realized how hard it would be to keep track of different
versions of the same custom functions scattered around different .R files. So i decided to grop them here.  

The DPLabR's functions cover different omics technologies, namely `Bulk RNAseq`, `ChIPseq`, `scRNAseq` and `Proteomics`. It's probably not straight forward to remember which function belong to which tech, so i'll try to be as exaustive as possible when writing the documentation.

## Installation

Get the latest stable `R` release from [CRAN](http://cran.r-project.org/). Note 
that you need to have `R >= 4.3`. You can get devel version of DPLabR from [GitHub](https://github.com/AndreaMariani-AM/DPLabR) with:

``` r
# install.packages("devtools")
devtools::install_github("AndreaMariani-AM/DPLabR")
```

## Example (undre dev)

This is a basic example which shows you how to solve a common problem for each tech.

### Combinatorial Indexing

If you have run our pipeline based on [Alevin-fry](https://github.com/COMBINE-lab/alevin-fry) pipeline then an intuitive to lead your experiment is to leverage `DPLabR::load_split_seq`, which internally uses `fishpond::loadFry` function and does some additional things like standardizing gene names and creating an object based on the specie you specify.  
Then, there's an optional function to add a sample info on the experiment if this is provided.
Read the docs for more

```r
# Load expr
sce <- load_split_seq(fryDir, outputFormat, expType)
# Add sample info
sce <- add_sample_info(sce, fryDir, bc_filter)
```

### ChIPseq

Some routine analysis you might want to do, is quantify your ChIPseq experiments for some features. We use `get_coverage_custom` function to compute average scores from a list of [bigwig](https://genome.ucsc.edu/goldenPath/help/bigWig.html) files across a list of genomic regions in [BED format](https://genome.ucsc.edu/FAQ/FAQformat.html#format1).