sarks

SArKS (Suffix Array Kernel Smoothing) is an algorithm for identifying sequence motifs correlated with numeric scores (such as differential expression statistics from RNA-seq experiments). The paper describing the algorithm may be found at:

https://academic.oup.com/bioinformatics/article-abstract/35/20/3944/5418797

A preprint of the article is also available on biorxiv at:

https://www.biorxiv.org/content/early/2018/10/25/133934

Installation

SArKS is implemented in Java (1.8 or greater) with interactive use facilitated through an R package built using rJava.

Once these dependencies have been installed and correctly configured, you can install sarks by running the following code within an R session:

## if you don't already have remotes installed, uncomment and run:
# install.packages('remotes')
library(remotes)
install_github('denniscwylie/sarks')
## alternatively, to build vignette as well, try uncommenting and running:
# install_github('denniscwylie/sarks', build_vignettes=TRUE)

Alternative installation: Java only

1. Copy sarks.jar from inst/java/ subdirectory of this repository to convenient location

2. Test the installation by going through the simulated data example using sarks.jar as described below

Using sarks

This project implements the SArKS algorithm in the java package contained in sarks.jar, which can also be run as part of the R package sarks.

Using the R package sarks

For most users, we would recommend trying out the R package, which can be installed as described above.

The sarks vignette is the best place to start to learn how to use the R version of sarks.

The full vignette is available as a pdf if you use the "build_vignettes=TRUE" option when installing sarks in R; otherwise, you can take a look at the abridged markdown vignette.

Direct command-line usage of jar file

For detailed information on command-line usage of sarks.jar and associated scripts, consult user_guide.md.

The best way to learn how to use sarks is to read through the example scripts

examples/*_example.sh

(markdown versions of each of the examples are available as well) included in the github repository.

These examples are taken from the data sets analyzed in the SArKS paper, including the toy simulated data set as well as the analyses of the upstream (5' of transcription start site) and downstream (3' of transcription start site) DNA regions for mouse genes whose expression profiles were quantified in the studies:

• Mo, Alisa, et al. "Epigenomic signatures of neuronal diversity in the mammalian brain." Neuron 86.6 (2015): 1369-1384.
• Close, Jennie L., et al. "Single-cell profiling of an in vitro model of human interneuron development reveals temporal dynamics of cell type production and maturation." Neuron 93.5 (2017): 1035-1048.

Simulated data example

The simulated data set consists of the 30 sequences contained in

• examples/simulated_seqs.fa

together with the associated scores contained in

• examples/simulated_scores.tsv

The file

examples/simulated_example.md

uses the utility scripts also contained in the examples folder to analyze these sequences and scores. After moving to the examples directory,

cd examples/

I recommend reading through the example and running the commands contained within individually at the command line as you get to them.

Mo 2015 downstream example

After going through the simulated example, try sarks out on the Mo 2015 downstream seqs. An example of how to do this can be found in the

examples/mo2015_downstream_example.md

file; again I would recommend reading through the example and running the commands line-by-line as you get to them.

Mo 2015 upstream example

NOTE: this example has been removed from the main sarks repository because of Bioconductor file size limitations; you can find it in the separate sarks_examples git repository.