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afs2dxo

basenji

Sequential regulatory activity predictions with deep convolutional neural networks.

bayesembler

A Bayesian method for doing transcriptome assembly from RNA-seq data

bio_corex

Bio CorEx

cactus

Official home of genome aligner based upon notion of Cactus graphs

chiron

A basecaller for Oxford Nanopore Technologies' sequencers

conda-package-handling-feedstock

A conda-smithy repository for conda-package-handling.

cpc2

Mirror of the CPC2 code.

dammit

just annotate it, dammit!

diamond

Accelerated BLAST compatible local sequence aligner.

dlpipeline

Practical Deep Learning for Genomic Prediction: A Keras based guide to implement deep learning

eager

A fully reproducible and state of the art ancient DNA analysis pipeline.

edta

Extensive de-novo TE Annotator

ei-annotation

ei-liftover

Repository to transfer gene models across (sub)genomes and check their coherence.

fastnumbers-feedstock

A conda-smithy repository for fastnumbers.

git-feedstock

A conda-smithy repository for git.

gts

Pipeline that filters transcripts in order to train augustus for non-model organisms

hifive

Tools for handling HiC and 5C data

ibspy

Python library to identify Identical By State regions

intervene

Fork of intervene at https://bitbucket.org/CBGR/intervene/overview

lucventurini.github.io

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

matplotlib-venn

Area-weighted venn-diagrams for Python/matplotlib

mica

MIcrobiomes using Compressive Acceleration

mikado

Mikado is a lightweight Python3 pipeline whose purpose is to facilitate the identification of expressed loci from RNA-Seq data and to select the best models in each locus.

mikado-analysis

Analyses and draft of the paper for Mikado.

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

nanosim

Nanopore sequence read simulator

oracle_trainer

Scripts to automate the training of Augustus, TwinScan, GeneID and SNAP.

orthofinder

Accurate inference of orthologous gene groups made easy. "OrthoFinder: solving fundamental biases in whole genome comparisons dramatically improves orthologous gene group inference accuracy"