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deepdependency

deepest-fusion

DEEPEST-Fusion is a fusion detection algorithm specially designed for screening massive cancer sequencing databases

demuxlet

Genetic multiplexing of barcoded single cell RNA-seq

dentil

A strategy to quantify the density of tumor-infiltrating lymohocytes

dndssimulator

dNdS Simulator uses R to simulate a stochastic branching process with a set of genotypes and phenotypes per cell. The main advantage of the model is that simulates immunoediting by introducing immunogenic and escape mutations as well as driver and passenger mutations

do

doabsolute

:package: Automate Absolute Copy Number Calling using 'ABSOLUTE' package

doing-meta-analysis-in-r

All R codes for the guide "Doing Meta-Analysis in R"

dorothea

R package to access DoRothEA's regulons

doseresponsepma

Bayesian dose-response pairwise- and network meta-analysis

doubletfinder

R package for detecting doublets in single-cell RNA sequencing data

dragonsc

Deterministic annealing gaussian mixtures models for single cell RNAseq

drews2022_cin_compendium

Main repository for Drews et al. (Nature, 2022)

dropest

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

easier

building and progression of easieR as an R metapackage using dialog box (only French version for now)

ega-data-api

ega-download-client

A basic Python-based EGA download client

egfr-structure-function-nature-manuscript

ena-fast-download

Download FASTQ files of reads from the European Nucleotide Archive (ENA)

engle_lab_alon

enlight-data

Datasets to accompanied ENLIGHT manuscript

enlight-deeppt-data

This repository contains data and other materials related to the DeepPT manuscript

ensemblesvm

A Library for Ensemble Learning Using Support Vector Machines

epic

Repository for the R package EPIC, to Estimate the Proportion of Immune and Cancer cells from bulk gene expression data.

epla

A multi-instance learning on pathological images to predict MSI

ervcaller

ERVcaller is a tool designed to accurately detect and genotype non-reference unfixed endogenous retroviruses (ERVs) and other transposable elements (TEs) in the human genome using next-generation sequencing (NGS) data. We evaluated the tools using both simulated and real benchmark whole-genome sequencing (WGS) datasets. ERVcaller is capable to accurately detect various TE insertions of any lengths, particularly ERVs. It allows for the use of a TE reference library regardless of sequence complexity, such as the entire RepBase database. It is easy to install and use with command lines.

ervmap

ERVmap is one part curated database of human proviral ERV loci and one part a stringent algorithm to determine which ERVs are transcribed in their RNA seq data.

esatac

Bioconductor package: An Easy-to-use Systematic pipeline for ATACseq data analysis

escc-code

ezcox

Easily Process a Batch of Cox Models