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abcd

alleledb

The package includes the AlleleDB pipeline developed in the Gerstein Lab at Yale. This pipeline was built and applied to perform a uniform identification of SNVs associated with allele-specific binding and expression in 382 individuals from the 1000 Genomes Project. Please see website for more detailed README.

alleleseq2

aloft

ALOFT, the Annotation Of Loss-of-Function Transcripts, provides extensive functional annotations to loss-of-function variants in the human genome.

annotation-k-mer-extractor

Using sliding window to extract k-mers for annotation (specfically exons) in GTF format

bay2ctrls

Bayesian model to integrate two types of ChIP-seq controls for binding site detection

biocoder

cbb752b19

CBB752 SP2019 Course Website

cbb752b20

cbb752b21

cbb752b22

cbb752b23

chromosomepaintingtool

Chromosome Painting Tool for visualizing signal track density heat-maps of ENTEx experiments.

chronode

dasthma

decoasthma

Code to reproduce the analyses described in the manuscript, "Approaches for integrating heterogeneous RNA-seq data reveals cross-talk between microbes and genes in asthmatic patients"

decode

A Deep-learning Framework for Condensing Enhancers and Refining Boundaries with Large-scale Functional Assays

deepvelo

dreiss

entexbert

The DNABERT model for ENTEx

esprnn

ESPRNN: Epigenome-based Splicing Prediction using Recurrent Neural Network

evotum101

Modelling tumor progression from a single VCF file

excerpt

Software for preprocessing, filtering, alignment, and reporting of smallRNA-seq datasets

factual_clinicalsumm

fancy

Predicting privacy risk of functional genomics data

fmgene

forest-fire-clustering

A clustering algorithm that can perform internal validation inspired by forest fire dynamics and self-organized criticality

frustration

funseq2

A flexible framework to annotate and prioritize cancer somatic mutations.

fusionseq

Identifying fusion transcripts by using paired-end RNA Sequencing