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amoebae

Workflow for identifying and classifying homologous gene/protein sequences

bismark

A tool to map bisulfite converted sequence reads and determine cytosine methylation states

bsvf

Bisulfite Sequencing Virus integration Finder

clinker

Gene cluster comparison figure generator

demo2-github

An example for students of BIOS606

gatk

Official code repository for GATK versions 4 and up

igv-reports

Python application to generate self-contained igv.js pages that can be opened within a browser with "file" protocol.

intervene

Intervene: a tool for intersection and visualization of multiple genomic region and gene sets

metaomgraph

MetaOmGraph: a workbench for interactive exploratory data analysis of large expression datasets

methpipe

A pipeline for analyzing DNA methylation data from bisulfite sequencing.

monod2

MONOD2 is a toolkit for methylation haplotype analysis of bisulfite sequencing data

nature_bash

Example scripts demonstrating science at the command line.

numetwg

pieces_of_code_for_bioinformatics

plant-virus-detection-pipeline

PVDP is an open source tool for the identification of plant viruses in RNA-seq data. This project was funded by Fondo de Ciencia, Tecnología e Innovación del Sistema General de Regalías del Departamento de Antioquia under grant 1101-805-62787 (Convenio No. 4600007658-779) and executed with the participation of Universidad Nacional de Colombia sede Medellín, Universidad CES and Fedepapa. The project was supervised by Secretaria de Agricultura de Antioquia and Ministerio de Ciencia, Tecnología e Innovación de Colombia.

pywgcna

PyWGCNA is a Python package designed to do Weighted correlation network analysis (WGCNA)

rna-seq-model-organism-plant

rnaseq

Fast RNAseq pipeline

shournal

A (file-) journal for your shell

statannotations

add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.

swiftortho

A high performance tool to identify orthologs and paralogs across genomes.

telescope

Quantification of transposable element expression using RNA-seq