bedtools

rnabioco/valr

Genome Interval Arithmetic in R

noamteyssier/gia

gia: Genomic Interval Arithmetic

davetang/defining_genomic_regions

Define regions in the genome

rpianezza/GenomeDelta

Detecting transposable element invasions without repeat library. Detects also horizontal transfer events and endogenized viruses. All you need is a reference genome and some short reads

KCCG/seave

Seave is a web platform that enables genetic variants to be easily filtered and annotated with in silico pathogenicity prediction scores and annotations from popular disease databases. Seave stores genomic variation of all types and sizes, and allows filtering for specific inheritance patterns, quality values, allele frequencies and gene lists. Seave is open source and deployable locally, or on a cloud computing provider, and works readily with gene panel, exome and whole genome data, scaling from single labs to multi-institution scale.

DEIB-GECO/PyGMQL

Python Library for data analysis based on GMQL

LBGC-CFB/SpliceLauncher

RNAseq pipeline for alternative splicing junctions

asadprodhan/A-beginner-s-guide-to-Bioinformatics

A beginner’s guide to Bioinformatics

jlanga/exfi

Get exons from a transcriptome and raw genomic reads using abyss-bloom and bedtools

muhligs/bed6ToBed12

program to make bed12 files from bed 6 files based on the name col of the bed6 file.

shencangsheng/pg_bedtools_rs

A PostgreSQL plugin for bedtools, implemented in Rust.

manojbhosale/ngsUtils

Useful NGS utilities for everyday use in the form of stand-alone tool.

afreeorange/autozygosity

A public, web-based homozygosity mapping tool

jazminvaleriano/RNAseq-differential-expression

Assembly of RNA transcriptome, differential expression analysis, identification of lncRNA candidates based on genomic context and protein coding potential.

ProfH2SO4/lumbridge

Plant DNA Annotation and Preparation for Neural Networks

saidmlonji/rnaseq_pipeline

RNA-seq pipeline in R/Bash enables QC, alignment, read counting, and differential expression using Bioconductor; reproducible workflow on Ubuntu with Conda. 🐙

AriannaRigamonti/Genomics

Pipeline for automated genomic variant analysis in inherited diseases, integrating alignment, variant calling, and quality control

CHRUdeLille/bedtools

bedtools environment containerized for singularity

daaaaande/bionanotator

bionano annovar annotation

halavah/picgo

Use by myself - PicGo

rgranit/merge-bed-batch

Run the bedtools merge command on multiple files

sebastian-gregoricchio/Rseb

An R-package for daily tasks required to handle biological data as well as avoid re-coding of small functions for quick but necessary data management.

utdal/Bulk-RNA-Seq-Nextflow-Pipeline

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.

asadprodhan/Gene_seq_extraction_from_multiple_genomes

How do I automate extracting multiple gene sequences from multiple genomes?

ataki/epigensML

Predicting Tissue Specific Enhancer Activity from Epigenetic Marks and Sequence

cyverseuk/bedtools

Grelot/reserveBenefit--snpsdata_analysis

Codes i wrote for the paper "genomic resources for Mediterranean fishes"

hisplan/docker-bedtools

Dockerized bedtools

jrhawley/bio-jtools

Various bioinformatics tools in one package

metamaden/seq_answers

Sequencing data preprocessing

unikill066/Bulk-RNA-Seq-Nextflow-Pipeline

This is an automated workflow pipeline for analyzing and processing Bulk-RNA seq data, implemented primarily in bash, python and R, and wrapped in a NextFlow workflow to characterize the gene landscape in the samples.