Repositories list

• awesome

  Public
  😎 Awesome lists about all kinds of interesting topics

  Creative Commons Zero v1.0 Universal

  •28k•0•0•0•Updated Apr 1, 2022Apr 1, 2022

• ncbi-genome-download

  Public
  Scripts to download genomes from the NCBI FTP servers

  Python

  •

  Apache License 2.0

  •175•0•0•0•Updated Mar 24, 2020Mar 24, 2020

• awesome-expression-browser

  Public
  😎 A curated list of software and resources for exploring and visualizing (browsing) expression data 😎

  software-packages

  MIT License

  •38•0•0•0•Updated Dec 25, 2019Dec 25, 2019

• Code_Cellar

  Public
  Collection of scripts and drafts mainly for NGS-related work.

  ngs-scripts

  R

  •0•0•0•0•Updated Dec 3, 2019Dec 3, 2019

• anna_utils

  Public
  mini-projects and utility functions that are useful across an array of projects that I am working on

  Jupyter Notebook

  •2•0•0•0•Updated Nov 23, 2019Nov 23, 2019

• RNA-seq_length_bias

  Public
  R

  •7•0•0•0•Updated Sep 4, 2019Sep 4, 2019

• Rscripts

  Public
  Random R scripts

  rscripts

  R

  •0•1•0•0•Updated Aug 7, 2019Aug 7, 2019

• Mfuzz_RNAseq

  Public
  A R script to perform clustering of gene expression time-series RNA-seq data with Mfuzz.

  rclustering

  R

  •3•0•0•0•Updated Apr 16, 2019Apr 16, 2019

• Brundle_Example

  Public
  Self Contained Examples of Functions for Brundle R package

  R

  •1•0•0•0•Updated Mar 26, 2019Mar 26, 2019

• MicroArray-to-logFC-GeneLists-Limma

  Public
  From gene expression microarray data to Limma and curation of resulting Gene Lists.

  R

  •1•0•0•0•Updated Jan 16, 2019Jan 16, 2019

• gff-annotation-tools

  Public
  Tools used for generation and annotation of .gff files with ChIP-seq, ATAC-seq, MNase-seq and bisulfite datasets.

  Perl

  •

  MIT License

  •2•1•0•0•Updated Aug 24, 2018Aug 24, 2018

• ChromosomeMappings

  Public
  This repository contains chromosome/contig name mappings between UCSC <-> Ensembl <-> Gencode for a variety of genomes.

  59•1•0•0•Updated Aug 20, 2018Aug 20, 2018

• Bioinformatics

  Public
  Bioinformatics analysis scripts, workflows, general code examples

  Shell

  •14•1•0•0•Updated Jul 25, 2018Jul 25, 2018

• forward

  Public
  Sherlock Port Forwarding Utility

  jupytersherlock

  Shell

  •27•0•0•0•Updated Jul 7, 2018Jul 7, 2018

• tss-annotation

  Public
  Simple reproducible managment of annotated TSS and gene bodies

  Shell

  •1•0•0•0•Updated Jun 7, 2018Jun 7, 2018

• bioinformatics-one-liners

  Public
  my collection of bioinformatics one liners that is useful in my day-to-day work

  MIT License

  •130•1•0•0•Updated Dec 30, 2017Dec 30, 2017

• bioconductor-transcript-length

  Public
  An exploration of methods for querying transcript length in Bioconductor.

  2•0•0•0•Updated Nov 8, 2017Nov 8, 2017

• oneliners

  Public
  Useful bash one-liners for bioinformatics.

  521•0•0•0•Updated Jun 26, 2017Jun 26, 2017

• Matrix-formatting-for-Cytoscape

  Public
  Converting an experimentally derived Spearman matrix into a Cytoscape compatible table

  R

  •1•0•0•0•Updated Jun 1, 2017Jun 1, 2017

• scripts-general-use

  Public
  HTML

  •

  MIT License

  •12•0•0•0•Updated May 21, 2017May 21, 2017

• batch-effect-analysis

  Public
  report on SVA performance in Batch Effect estimation

  R

  •1•0•0•0•Updated Apr 5, 2017Apr 5, 2017

• R_snippets

  Public
  R Scripts for general data analysis and plotting

  R

  •144•0•0•0•Updated Aug 3, 2016Aug 3, 2016

• KTools

  Public
  some tools used for different analysis

  Perl

  •2•0•0•0•Updated Jun 24, 2015Jun 24, 2015

• motif-search-significance

  Public
  motif

  Perl

  •1•0•0•0•Updated Mar 20, 2015Mar 20, 2015

• misc

  Public
  miscellaneous scripts

  scripts

  Perl

  •3•0•0•0•Updated Oct 6, 2014Oct 6, 2014