Discover SchulzLab/EpigenomeAnalysisTutorial-2020 Open Source project

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Python
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Created about 4 years ago
Updated about 4 years ago

SchulzLab

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This website contains material for an epigenome analysis tutorial that covers ATAC-seq analysis and integration with TF motifs and gene expression

TEPIC

Annotation of genomic regions using transcription factor binding sites and epigenetic data

Python

ORNA

Fast in-silico normalization algorithm for NGS data

C++

EpigenomicsTutorial-ISMB2017

Repository for the Epigenomics Tutorial hold at ISMB 2017 in Prague

Shell

STARE

TF analysis from epigenetic and Hi-C data

C++

STITCHIT

Learning gene-specific regulatory elements from epigenetic data

HTML

Aeron

Alignment, quantification and fusion prediction from long RNA reads

Python

RAPID

RAPID is a set of tools for the alignment, and analysis of genomic regions with small RNA clusters derived from small RNA sequencing data.

HTML

SNEEP

SNp Exploration and Analysis using EPigenomics data

C++

KREATION

automated k-mer range estimation for de novo transcriptome assembly

Python

Triangulate

Inferring regulators from single cell RNA-seq data

OntologyEval

OntologyEval is an approach that can be used to compare batch effect correction of normalisation methods for cell heterogeneous genome-wide datasets, like RNA-seq. It uses the cell ontology to evaluate whether datasets derived from different cell types are similar to one another.

TriplexAligner

A method for sequence based prediction of RNA-DNA triplices.

SOS

Automated de novo transcriptome assembly

Python

MASSIF

Improved motif enrichment analysis using protein domain type information

HTML

JAMI

Java tool for computing conditional mutual information from large datasets

Java

SingleCellStitchit

Learning enhancer-gene interactions from single cell data

C++

SplitOrfs

A workflow to computationally detect transcripts that could generate several distinct ORFs that match to the same protein. This can be used to find for example nonsense-mediated decay transcripts that make more than one ORF.

Python

TFML

Makefile

RJAMI

R-wrapper for JAMI: Computation of conditional mutual information from large datasets

TFAnalysis

processing and analysis of transcription factor binding sites

Python

Codefinder

Learning translation code between sets of DNA motifs

SchulzLab/EpigenomeAnalysisTutorial-2020

SchulzLab

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