## iscream <a href="https://huishenlab.github.io/iscream/"><img src="man/figures/logo.png" align="right" height="138" style="float:right; height:138px;"/></a>

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iscream aims to efficiently read data from any BED file into formats usable by
other packages. Using [htslib](https://www.htslib.org/), iscream can query
genomic regions like [tabix](https://en.wikipedia.org/wiki/Tabix), summarize the
queried data and make matrices, with specific support for WGBS BED files aligned
by [BISCUIT](https://huishenlab.github.io/biscuit/),
[Bismark](https://www.bioinformatics.babraham.ac.uk/projects/bismark/) and
[BSBolt](https://bsbolt.readthedocs.io/en/latest/).

Analysis and visualization of Whole Genome Bisulfite Sequencing (WGBS)[^1] data
requires reading aligned sequencing data into formats that existing packages
like [BSseq](https://bioconductor.org/packages/devel/bioc/html/bsseq.html) and
[scMET](https://github.com/andreaskapou/scMET) can analyze. Getting the data
from on-disk BED files to a matrix of methylation values can be difficult
because, with nearly 30 million CpGs, WGBS data can be quite large. iscream
makes importing WGBS data for targeted exploration and analysis faster and more
memory efficient.

[^1]: The name iscream comes from "*Integrating Single-Cell Results for
Exploring and Analyzing Methylation*" as it was originally developed to read BED
files from WGBS. It was then generalized to work with any BED file.


## Dependencies

### *htslib* >= 1.17

*iscream* depends on the *htslib* header files. These may be installed with
your package manager:

- ubuntu/debian: `libhts-dev`  
- fedora/RHEL: `htslib-devel`  
- brew: `htslib`  
- nixpkgs: `htslib`
- conda: `bioconda::htslib`

or built manually: <https://www.htslib.org/download/>. *iscream* can use
*Rhtslib* as the htslib source but we recommend installing htslib with
libdeflate support for optimal performance - see
[`vignette("htslib")`](https://huishenlab.github.io/iscream/articles/htslib.html)
for more information.


The header files may also be found among your HPC modules - make sure the
`PKG_CONFIG_PATH` environment variable includes the `pkgconfig` location for
your installation of *htslib*. You can verify that the *htslib* development
libraries are installed with `pkg-config`:

```bash
# set path if necessary
export PKG_CONFIG_PATH=[path to htslib installation]
# verify that htslib can be found
pkg-config --cflags --libs htslib
```

#### *tabix*

Some *htslib* installations do not include the *tabix* executable (on Ubuntu you
need to install both *libhts-dev* and *tabix*). *iscream* will work without
*tabix*, but the `tabix()` function will be faster if the executable is
installed.

### GCC >= 9.4.0

GNU GCC must be installed for OpenMP support. This is usually installed by
default on Linux systems, but may need to be manually installed on MacOS to use
iscream with multiple threads[^2].

[^2]: Using OpenMP is also possible with Clang on MacOS
(<https://mac.r-project.org/openmp/>) but installing GCC with Homebrew may be
easier (<https://formulae.brew.sh/formula/gcc>).

## Installation

### Bioconductor

```r
if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")
BiocManager::install("iscream")
```

### GitHub

You can install the development version from Github by cloning the repo and
running

```bash
git clone https://github.com/huishenlab/iscream
R CMD INSTALL iscream
```

You can also use the R [`devtools`](https://devtools.r-lib.org/) package:

```r
devtools::install_github("huishenlab/iscream")
```

or [`pak`](https://pak.r-lib.org/):

```r
pak::pkg_install("huishenlab/iscream")
```

### Usage

See the [quick start guide](https://huishenlab.github.io/iscream/articles/iscream.html)
for an overview of iscream's functionality and the [function reference](https://huishenlab.github.io/iscream/reference/)
for all available functions. Bug reports may be submitted through [GitHub issues](https://github.com/huishenlab/iscream/issues).
