Repositories list

• RLPipes

  Public
  RLPipes: A standardized R-loop-mapping pipeline.

  snakemaker-loopbioinformatics+ 2pipelinengs

  Python

  •

  MIT License

  •1•3•13•0•Updated May 22, 2024May 22, 2024

• autoPLIER-analysis

  Public
  Analysis for the autoPLIER project

  Jupyter Notebook

  •1•2•15•0•Updated Feb 8, 2023Feb 8, 2023

• RLSeq

  Public
  An analysis package for R-loop mapping data

  bioinformaticsbioconductorr-loop+ 3rrstatsr-package

  R

  •

  Other

  •0•2•6•0•Updated Jan 11, 2023Jan 11, 2023

• RLBase-data

  Public
  Protocol for building/updating RLBase

  R

  •

  MIT License

  •0•1•14•0•Updated Aug 9, 2022Aug 9, 2022

• bioconda-recipes

  Public
  Conda recipes for the bioconda channel.

  Shell

  •

  MIT License

  •3.3k•0•0•0•Updated Aug 8, 2022Aug 8, 2022

• RA-Eval

  Public
  Task for evaluating skill level of Bioinformatics RA candidates.

  R

  •0•1•0•0•Updated Jul 28, 2022Jul 28, 2022

• RLSuite-Paper-Miller-2022

  Public
  Code used to generate figures in the RLSuite paper

  HTML

  •

  MIT License

  •0•1•0•0•Updated Jul 8, 2022Jul 8, 2022

• autoplieR

  Public
  R port of autoplier

  R

  •

  Other

  •0•0•1•0•Updated Jul 6, 2022Jul 6, 2022

• RLoop-QC-Meta-Analysis-Miller-2022

  Public
  Generates figures for "Quality-controlled R-loop meta-analysis reveals the characteristics of R-loop consensus regions"

  bioinformaticsr-loops

  R

  •0•0•20•0•Updated Jul 2, 2022Jul 2, 2022

• RLBase

  Public
  RLBase: A database of R-loops and R-loop-mapping experiments

  R

  •

  MIT License

  •0•2•6•1•Updated Jun 28, 2022Jun 28, 2022

• correlationAnalyzeR-ShinyApp

  Public
  A web application interface for correlationAnalyzeR

  shiny-servershiny

  R

  •0•1•3•0•Updated Jun 27, 2022Jun 27, 2022

• correlationAnalyzeR

  Public
  Generate Novel Insights from Gene Correlation Data

  bioinformaticsrna-seqanalysis+ 3msigdbgene-setgene-correlation-data

  R

  •6•10•5•0•Updated Jun 27, 2022Jun 27, 2022

• LiverDB

  Public
  HTML

  •

  MIT License

  •0•0•0•0•Updated Jun 23, 2022Jun 23, 2022

• Cell-Compass

  Public
  HTML

  •0•0•0•0•Updated Feb 3, 2022Feb 3, 2022

• FibroDB

  Public
  Explore RNA-Sequencing results in fibroblast tissues

  HTML

  •

  MIT License

  •1•0•0•0•Updated Jan 20, 2022Jan 20, 2022

• RLHub

  Public
  ExperimentHub for accessing RLBase data

  bioinformaticsbioconductorr-package+ 1r

  R

  •

  Other

  •0•0•1•0•Updated Jan 20, 2022Jan 20, 2022

• onto_lib

  Public
  Tools for loading and manipulating ontologies in Python

  Python

  •

  MIT License

  •1•0•0•0•Updated Jul 3, 2021Jul 3, 2021

• Server-side-utilities

  Public
  Helper functions for server-side operations

  Shell

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 4, 2021Mar 4, 2021

• ewing_sarcoma_miller_cancers_2020

  Public
  Scripts and data for reproducing analysis in Miller et al. 2020

  data-miningcancer-genomicsrna-seq-analysis+ 2manifold-learningcancer-research

  R

  •1•3•0•0•Updated Nov 28, 2020Nov 28, 2020

• BishopLab_HTS_Pipeline

  Public
  Pipeline for automation of common HTS analysis tasks (e.g., RNA-Seq alignment)

  R

  •0•0•0•0•Updated Nov 28, 2020Nov 28, 2020

• getsysreqs

  Public
  Determine system requirements from R packages using the RStudio Package Manager. This is a weekend project, not a real package, so please think twice before using it for anything serious.

  R

  •

  Other

  •2•0•0•0•Updated Nov 2, 2020Nov 2, 2020

• S3norm

  Public
  An normalization method that can normalize high signals without inflate the background noise.

  Python

  •

  MIT License

  •3•0•0•0•Updated Jun 5, 2020Jun 5, 2020