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appliedgenomics2017

JHU EN.600.649: Computational Genomics: Applied Comparative Genomics

appliedgenomics2018

Materials for Spring 2018 Applied Genomics Course

armor

Light-weight Snakemake workflow for preprocessing and statistical analysis of RNA-seq data

artemis

Artemis is a free genome viewer and annotation tool that allows visualization of sequence features and the results of analyses within the context of the sequence, and its six-frame translation

augustus

Genome annotation with AUGUSTUS

bamtools

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

bandage

a Bioinformatics Application for Navigating De novo Assembly Graphs Easily

bash_scripts

Custom-made bash scripts

bedtools2

A powerful toolset for genome arithmetic.

bioconvert

Bioconvert is a collaborative project to facilitate the interconversion of life science data from one format to another.

bioinfinvrepro

repositorio de apuntes y código del curso "Introducción a la bioinformática e investigación reproducible para análisis genéticos"

bioinformatics-training

Bioinformatics training resources

canu

A single molecule sequence assembler for genomes large and small.

cdsb_test

test de repo

checkm

Assess the quality of microbial genomes recovered from isolates, single cells, and metagenomes

cnspipeline

comparative_genomics

Micro 612 genomics workshop

containers

Bioinformatics containers

corset

Software for clustering de novo assembled transcripts and counting overlapping reads

d3heatmap

A D3.js-based heatmap htmlwidget for R

deepbinner

a signal-level demultiplexer for Oxford Nanopore reads

deepmod

DeepMod: a deep-learning tool for genomic-scale, strand-sensitive and single-nucleotide based detection of DNA modifications

deepsignal

Detecting methylation using signal-level features from Nanopore sequencing reads

diamond

Accelerated BLAST compatible local sequence aligner.

dsbook

Repository for data science book

dyngenie3

Semi-parametric approach for the inference of gene regulatory networks from time series of expression data

easyfig

Development version of Easyfig

fgmp

Fungal Genome Mapping Pipeline

filtlong

quality filtering tool for long reads