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Vithusan Suppiyar (vsuppiyar)

vsuppiyar

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Company:@koppsteinlab (DKTK/DKFZ)

Location:Group for Cancer Bioinformatics and Multiomics, Düsseldorf

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Vithusan Suppiyar's starred repositories

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

License:MITStargazers:3055Issues:0Issues:0

awesome-nanopore

A curated list of awesome nanopore analysis tools.

License:MITStargazers:224Issues:0Issues:0

genomic-data-visualization-2024

Course website for Genomic Data Visualization 2024

Language:JavaScriptStargazers:22Issues:0Issues:0

ClinCNV

Detection of copy number changes in Germline/Trio/Somatic contexts in NGS data

Language:RLicense:MITStargazers:71Issues:0Issues:0

megSAP

a Medical Genetics Sequence Analysis Pipeline

Language:PHPLicense:GPL-3.0Stargazers:67Issues:0Issues:0

megLR

Snakemake workflow for comprehensive ONT analysis

Language:PythonStargazers:3Issues:0Issues:0

m6ABasecaller

An m6A-aware basecalling model to detect m6A modifications at single nucleotide resolution in individual reads (Cruciani, Delgado-Tejedor, Pryszcz et al., BioRxiv 2023)

Language:Jupyter NotebookLicense:GPL-3.0Stargazers:13Issues:0Issues:0

tombo

Tombo is a suite of tools primarily for the identification of modified nucleotides from raw nanopore sequencing data.

Language:PythonLicense:NOASSERTIONStargazers:226Issues:0Issues:0

nanocompore

RNA modifications detection from Nanopore dRNA-Seq data

Language:PythonLicense:GPL-3.0Stargazers:78Issues:0Issues:0

EpiNano

Detection of RNA modifications from Oxford Nanopore direct RNA sequencing reads (Liu*, Begik* et al., Nature Comm 2019)

Language:PythonLicense:GPL-2.0Stargazers:109Issues:0Issues:0

tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

Language:RLicense:GPL-3.0Stargazers:49Issues:0Issues:0

nanopolish

Signal-level algorithms for MinION data

Language:C++License:MITStargazers:553Issues:0Issues:0

IsoQuant

Transcript discovery and quantification with long RNA reads (Nanopores and PacBio)

Language:PythonLicense:NOASSERTIONStargazers:135Issues:0Issues:0

NanoCount

EM based transcript abundance from nanopore reads mapped to a transcriptome with minimap2

Language:PythonLicense:MITStargazers:53Issues:0Issues:0

htseq

HTSeq is a Python library to facilitate processing and analysis of data from high-throughput sequencing (HTS) experiments.

Language:C++License:GPL-3.0Stargazers:120Issues:0Issues:0

igv

Integrative Genomics Viewer. Fast, efficient, scalable visualization tool for genomics data and annotations

Language:JavaLicense:MITStargazers:628Issues:0Issues:0

graphmap2

GraphMap - A highly sensitive and accurate mapper for long, error-prone reads http://www.nature.com/ncomms/2016/160415/ncomms11307/full/ncomms11307.html https://www.biorxiv.org/content/10.1101/720458v1

Language:C++License:MITStargazers:65Issues:0Issues:0

minimap2

A versatile pairwise aligner for genomic and spliced nucleotide sequences

Language:CLicense:NOASSERTIONStargazers:1741Issues:0Issues:0

dorado

Oxford Nanopore's Basecaller

Language:C++License:NOASSERTIONStargazers:463Issues:0Issues:0

deeplexicon

Signal based nanopore RNA demultiplexing with convolutional neural networks

Language:Jupyter NotebookLicense:MITStargazers:34Issues:0Issues:0

master_of_pores

Nextflow pipeline for analysis of direct RNA Nanopore reads

Language:NextflowLicense:MITStargazers:88Issues:0Issues:0

MOP2

Master of Pores 2

Language:NextflowLicense:MITStargazers:22Issues:0Issues:0

NanoPlot

Plotting scripts for long read sequencing data

Language:PythonLicense:MITStargazers:403Issues:0Issues:0