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2brad_gatk

Genome-wide reference-based genotyping with 2bRAD

360yunpan

360YunPan Command-line tools, support: Linux Mac Windows

aaron

An R package of functions I use day-to-day in analysing various next-generation sequencing data, in particular whole genome bisulfite sequencing.

aasra

AASRA the comprehensive solution for small RNA alignment

abc

Allele-specific Binding from Chip-seq

academicpages.github.io

Github Pages template for academic personal websites, forked from mmistakes/minimal-mistakes

acfs

A pipeline for de novo circRNA identification

activedriverwgs

aligater

Software suite for detection/analysis of chimeric RNAs from LIGR-seq data

alleledb

The package includes the AlleleDB pipeline developed in the Gerstein Lab at Yale. This pipeline was built and applied to perform a uniform identification of SNVs associated with allele-specific binding and expression in 382 individuals from the 1000 Genomes Project. Please see website for more detailed README.

altanalyze

AltAnalyze is a multi-functional and easy-to-use software package for automated single-cell and bulk gene and splicing analyses. Easy-to-use precompiled graphical user-interface versions available from our website.

ancestry

program to estimate admixture coefficients from individual genotype or sequence data

aneva-dot

Tests Allelic Expression data for extreme imbalance w.r.t. population

apa

apa: research platform for the study of alternative polyadenylation, expressRNA.org

apalyzer

APAlyzer is a toolkit for bioinformatic analysis of alternative polyadenylation (APA) events using RNA sequencing data. Our main approach is comparison of sequencing reads in regions demarcated by high quality polyadenylation sites (PASs) annotated in the PolyA_DB database (http://exon.njms.rutgers.edu/polya_db/v3/). The current version (v3.0) uses RNA-seq data to examine APA events in 3’ untranslated regions (3’UTRs) and in introns. The coding regions are used for gene expression calculation.

aparent

APA Regression Net - Predict and Engineer Alternative Polyadenylation

arnapipe

atac-pipe

Analysis pipeline for ATAC-seq Data

atac-seq

Basic workflow for ATAC-seq analysis

ats-motif-prediction

This algorithm predicts RBP motifs based on target site accessibility in bound (positive) and unbound (negative) transcripts.

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

babelomics

bam2x

extract information from bam (sequence alignment) files and generate tables for further analysis.

bamtobw

Convert BAM files to bigWig files with a simple command

bamtools

C++ API & command-line toolkit for working with BAM data

barrettsprogressionrisk

Process and predict risk of adenocarcinoma progression from shallow whole-genome sequencing data.

basset

Convolutional neural network analysis for predicting DNA sequence activity.

bedtools-python

A Python interface to the BEDTools API using Cython

benchmarking_scripts

Repository to benchmark algorithms for determining expressed full length mRNA splice forms from RNA-seq data.

bio-viennangs

A Perl extension and collection of utilities for Next-Generation Sequencing (NGS) data analysis