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denovo-variant-caller-java

A de novo variant caller which uses information from a mother, father and child trio with a bayesian inference method.

deploid-r

An R interface for dEploid. dEploid is designed for deconvoluting mixed genomes with unknown proportions. Traditional ‘phasing’ programs are limited to diploid organisms. Our method modifies Li and Stephen’s algorithm with Markov chain Monte Carlo (MCMC) approaches, and builds a generic framework that allows haloptype searches in a multiple infection setting.

deseq2

This is a read-only mirror of the Bioconductor SVN repository. Package Homepage: http://bioconductor.org/packages/devel/bioc/html/DESeq2.html Bug Reports: https://support.bioconductor.org/p/new/post/?tag_val=DESeq2.

detonate

DETONATE: DE novo TranscriptOme rNa-seq Assembly with or without the Truth Evaluation

developments-in-next-generation-sequencing

Developments in next generation sequencing: instruments, read lengths, throughput. See

devtools

Tools to make an R developer's life easier

diffrepeats

Quantify repeat element enrichment with next-generation sequencing data

diffreps

Differential analysis for ChIP-seq with biological replicates

digenome-toolkit

Digenome Toolkit

distmap

DistMap

dmtk

Microsoft Distributed Machine Learning Toolkit

dnc

Differentiable Neural Computers

dnmf

Discriminant Nonnegative Matrix Factorization

docker

Docker - the open-source application container engine

docker-bioconda

Bioconda base container for easy bioinformatic tool installation

docker-brew-ubuntu-core

Official imports of the Ubuntu Core tarballs for use in Docker

docker-galaxy-stable

:whale::bar_chart::books: Docker Images tracking the stable Galaxy releases.

docker-ipython-notebook

:whale: :microscope: :books: IPython running in a docker container. This image can be used to integrate IPython into Galaxy

docker-jbrowse

Docker image of JBrowse Genome Browser

docker-pyclone

docker-recipes

:whale: Dockerfiles to build Galaxy images

docker-stacks

Opinionated stacks of ready-to-run Jupyter applications in Docker.

docker-varscan-cwl

Combination varscan/samtools container for easier running in workflows.

dockerflow

Dockerflow is a workflow runner that uses Dataflow to run a series of tasks in Docker with the Pipelines API

dogs

Analysis notebooks

downhill

Stochastic gradient routines for Theano

dp

A deep learning library for streamlining research and development using the Torch7 distribution.

dplyr

Dplyr: A grammar of data manipulation

dream9_broad_challenge_scoring

This is the scoring application for the DREAM 9 Broad Gene Essentiality Prediction Challenge.

dream9_broad_challenge_scoring-1

This is the scoring application for the DREAM 9 Broad Gene Essentiality Prediction Challenge.