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Utility for FAST counting splice site junctions and related information from BAM files.
Mayo Clinic CAP miRNAseq
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.
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.
Code for Expression in arrays and Seq
Validate FastQ Files
A model to identify organisms present in metagenomes in seconds
Useful set of classes for creating statistical genetic programs.
Docker Official Image packaging for MariaDB
tweaks to mirdeep2 for saner output
MOdel-based one and two Sample Analysis and Inference for ChIP-Seq
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
python module to plot beautiful and highly customizable genome browser tracks
Python implementation of SAML2
Pipeline scripts to align reads generated by RASL-seq
scTyper: a comprehensive pipeline for the cell typing analysis of single-cell RNA-seq data
Pipeline for analysis of SEQ data from the UCLA sequencing core, using STAR as main aligner and htseq-count
Helpful R functions
A declarative, efficient, and flexible JavaScript library for building user interfaces.
🖖 Vue.js is a progressive, incrementally-adoptable JavaScript framework for building UI on the web.
TypeScript is a superset of JavaScript that compiles to clean JavaScript output.
An Open Source Machine Learning Framework for Everyone
The Web framework for perfectionists with deadlines.
A PHP framework for web artisans
Bring data to life with SVG, Canvas and HTML. 📊📈🎉
JavaScript (JS) is a lightweight interpreted programming language with first-class functions.
Some thing interesting about web. New door for the world.
A server is a program made to process requests and deliver data to clients.
Machine learning is a way of modeling and interpreting data that allows a piece of software to respond intelligently.
Some thing interesting about visualization, use data art
Some thing interesting about game, make everyone happy.
We are working to build community through open source technology. NB: members must have two-factor auth.
Open source projects and samples from Microsoft.
Google ❤️ Open Source for everyone.
Alibaba Open Source for everyone
Data-Driven Documents codes.
China tencent open source team.