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altsplicingmodel

bam2ssj

Utility for FAST counting splice site junctions and related information from BAM files.

cap_mirnaseq

Mayo Clinic CAP miRNAseq

chipqc_bioc3.4

ctcsmodel

When messenger RNA splicing occurs co-transcriptionally, the potential for kinetic control based on transcription dynamics is widely recognized. Indeed, perturbation studies have reported that when transcription kinetics are perturbed genetically or pharmacologically splice patterns may change. However, whether kinetic control is contributing to the control of splicing within the normal range of physiological conditions remains unknown. We examined if the kinetic determinants for co-transcriptional splicing (CTS) might be reflected in the structure and expression patterns of the genome and epigenome. To identify and then quantitatively relate multiple, simultaneous CTS determinants, we constructed a scalable mathematical model of the kinetic interplay of RNA synthesis and CTS and parameterized it with diverse next generation sequencing (NGS) data. We thus found a variety of CTS determinants encoded in vertebrate genomes and epigenomes, and that these combine variously for different groups of genes such as housekeeping versus regulated genes. Together, our findings indicate that the kinetic basis of splicing is functionally and physiologically relevant, and may meaningfully inform the analysis of genomic and epigenomic data to provide insights that are missed when relying on statistical approaches alone.

demultiplex

diffbind

This is a branch from the mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/DiffBind.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=DiffBind.

exonpipeline

expression

Code for Expression in arrays and Seq

fastqc

fastqvalidator

Validate FastQ Files

focus

A model to identify organisms present in metagenomes in seconds

libstatgen

Useful set of classes for creating statistical genetic programs.

macs2-2.1.1.20160309

mariadb

Docker Official Image packaging for MariaDB

mirdeep2

tweaks to mirdeep2 for saner output

mosaics

MOdel-based one and two Sample Analysis and Inference for ChIP-Seq

pangolin

Software package for assigning SARS-CoV-2 genome sequences to global lineages.

pygenometracks

python module to plot beautiful and highly customizable genome browser tracks

pysaml2

Python implementation of SAML2

rasl_align

Pipeline scripts to align reads generated by RASL-seq

sctyper

scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data

seq_pipeline

Pipeline for analysis of SEQ data from the UCLA sequencing core, using STAR as main aligner and htseq-count

superfocus

useful_r

Helpful R functions