Here are
89 public repositories
matching this topic...
Signal-level algorithms for MinION data
Deep learning infrastructure for genomics
Updated
Jun 28, 2021
Jupyter Notebook
Analysis Pipeline for Single Cell ATAC-seq
Single-cell Transcriptome and Regulome Analysis Pipeline
Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.
Updated
May 20, 2021
Python
Deep neural networks for predicting CpG methylation
Updated
Sep 30, 2019
Python
Megalodon is a research command line tool to extract high accuracy modified base and sequence variant calls from raw nanopore reads by anchoring the information rich basecalling neural network output to a reference genome/transriptome.
Updated
Jul 22, 2021
Python
WGBS/NOMe-seq Data Processing & Differential Methylation Analysis
Updated
Jul 2, 2021
Python
Detecting methylation using signal-level features from Nanopore sequencing reads
Updated
Apr 5, 2021
Python
R package for Inference of differentially methylated regions (DMRs) from bisulfite sequencing
mgatk: mitochondrial genome analysis toolkit
Updated
Jun 28, 2021
Python
Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline
Updated
Apr 22, 2021
HTML
Code for the paper "Integrating regulatory DNA sequence and gene expression to predict genome-wide chromatin accessibility across cellular contexts"
Updated
Jun 9, 2021
Jupyter Notebook
A preprocessing and QC pipeline for HiChIP data
Updated
Jun 12, 2020
HTML
Cell type specific enrichments using finemapped variants and quantitative epigenetic data
Bead single-cell atac processing
Updated
May 26, 2020
Python
Modelling DNA methylation profiles
Enhancer Linking by Methylation/Expression Relationship (ELMER) is package to identify tumor-specific changes in DNA methylation within distal enhancers, and link these enhancers to downstream target genes
Python package to analyze DNA methylation data
Updated
Sep 22, 2020
Python
Preprocessing pipeline for (sc)ATAC data
Updated
Jul 11, 2020
Python
Simple web browser to visualize HiC tracks
Updated
Dec 12, 2019
JavaScript
R/Bioconductor package for optimized functional annotation of ChIP-seq data
Bioinformatic tools (R scripts) for the analysis of Absolute Quantification of Architecture (AQuA-HiChIP) style data.
CWL based Bioinformatics Workflows
Updated
Jul 21, 2021
Common Workflow Language
Bacterial Epigenomics Analysis SuiTe
BioWardrobe: an integrated platform for analysis of epigenomics and transcriptomics data
Updated
Apr 29, 2020
JavaScript
A Snakemake-based pipeline for gene mapping in Triticeae.
Updated
Jun 9, 2021
Python
Toolkit for concretely describing non-canonical DNA, RNA, and proteins
Updated
Oct 5, 2020
Python
EpiMethEx (Epigenetic Methylation and Expression), a R package to perform a large-scale integrated analysis by cyclic correlation analyses between methylation and gene expression data.
Computational inference of epimutation rates and spectra from high-throughput DNA methylation data in plants
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