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Open Sustainable Technology

https://github.com/afrendeiro/toolkit

A toolkit for NGS analysis with Python
atac-seq bioinformatics chip-seq looper ngs ngs-analysis project-management pypiper rna-seq
Added: over 1 year ago - Last Synced: about 1 year ago - Created: May 30, 2017

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 680
  • Committers: 3
  • Issues: 55
  • Pull Requests: 14
  • Owner: afrendeiro
  • Stars: 13
  • Forks: 4
  • Packages: 1
  • Downloads: 137
https://github.com/epigen/dea_limma

A Snakemake workflow for performing and visualizing differential expression analyses (DEA) on NGS data powered by the R package limma.
atac-seq bioinformatics biomedical-data-science chip-seq differential-expression-analysis limma limma-trend limma-voom r rna-seq scrna-seq snakemake statistics visualization volcano-plot workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 12, 2022

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: R
  • Commits: 47
  • Committers: 3
  • Issues: 9
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 14
  • Forks: 0
  • Packages: 0
https://github.com/epigen/spilterlize_integrate

A Snakemake workflow to split, filter, normalize, integrate and select highly variable features of count matrices resulting from experiments with sequencing readout (e.g., RNA-seq, ATAC-seq, ChIP-seq, Methyl-seq, miRNA-seq,...) including diagnostic visualizations.
atac-seq batch-effect bioinformatics biomedical-data-science chip-seq count-matrix dimensionality-reduction integration ngs normalization pipeline rna-seq snakemake visualization workflow
Added: over 1 year ago - Last Synced: about 1 year ago - Created: June 28, 2023

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 22
  • Committers: 2
  • Issues: 7
  • Pull Requests: 0
  • Owner: epigen
  • Stars: 8
  • Forks: 0
  • Packages: 0
https://github.com/guma44/geoparse

Python library to access Gene Expression Omnibus Database (GEO)
bioinformatics geo-database high-throughput-sequencing htseq microarray rna-seq rna-sequencing
Added: over 1 year ago - Last Synced: about 1 year ago - Created: August 16, 2015

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Jupyter Notebook
  • Commits: 212
  • Committers: 21
  • Issues: 58
  • Pull Requests: 25
  • Owner: guma44
  • Stars: 131
  • Forks: 49
  • Packages: 2
  • Downloads: 11,512
https://github.com/weng-lab/umitools

A toolset for handling sequencing data with unique molecular identifiers (UMIs)
bioinformatics high-throughput-sequencing rna-seq small-rna umi unique-molecular-identifier
Added: over 1 year ago - Last Synced: about 1 year ago - Created: February 16, 2016

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Python
  • Commits: 117
  • Committers: 3
  • Issues: 7
  • Pull Requests: 0
  • Owner: weng-lab
  • Stars: 14
  • Forks: 3
  • Packages: 1
  • Downloads: 64
https://github.com/poseidonchan/tape

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)
bioinformatics cell-composition-analysis cell-type-specific-gene-expression-analysis computational-biology deep-learning machine-learning precision-medicine rna-seq single-cell-analysis
Added: over 1 year ago - Last Synced: about 1 year ago - Created: July 15, 2021

  • Relevant topics? true
  • External users? true
  • Open source license? true
  • Active? true
  • Fork? false
  • Main Language: Jupyter Notebook
  • Commits: 102
  • Committers: 3
  • Issues: 10
  • Pull Requests: 5
  • Owner: poseidonchan
  • Stars: 42
  • Forks: 10
  • Packages: 1
  • Downloads: 146