Repositories list

• nf-alignment

  Public
  Nextflow based alignment pipeline

  Nextflow

  •1•1•0•0•Updated Mar 6, 2025Mar 6, 2025

• nf-referencebuilder

  Public
  Nextflow

  •1•0•0•0•Updated Mar 6, 2025Mar 6, 2025

• clarityclient2

  Public
  EE10 and modularisation update to the Java Clarity Client.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Mar 5, 2025Mar 5, 2025

• multiqc_mga2_plugin

  Public
  MultiQC Plugin for MGA 2

  Python

  •

  MIT License

  •0•1•0•0•Updated Mar 4, 2025Mar 4, 2025

• MultiQC

  Public
  Aggregate results from bioinformatics analyses across many samples into a single report.

  JavaScript

  •

  GNU General Public License v3.0

  •612•0•0•0•Updated Mar 4, 2025Mar 4, 2025

• nf_preprocess_scSeq_CRUKCI

  Public
  Download single cell data from Genomics server and process with CellRanger - specific to CRUK CI infrastructure

  Groovy

  •

  MIT License

  •0•0•0•0•Updated Feb 19, 2025Feb 19, 2025

• ampliconseq

  Public
  Variant calling pipeline for amplicon sequencing data

  R

  •0•4•0•0•Updated Jan 21, 2025Jan 21, 2025

• nextflow-support

  Public
  Scripts and functions that are helpful in Nextflow pipelines.

  Groovy

  •

  MIT License

  •0•0•0•0•Updated Nov 27, 2024Nov 27, 2024

• mga2

  Public
  Multi-genome alignment contaminant screen for high-throughput sequence data

  Rust

  •

  MIT License

  •1•3•0•0•Updated Nov 18, 2024Nov 18, 2024

• clarityclient

  Public
  A Java client for working with Genologics' REST API.

  Java

  •

  GNU General Public License v3.0

  •4•5•0•0•Updated Oct 23, 2024Oct 23, 2024

• clarityclient-recorder

  Public
  A recording and playback wrapper around our ClarityClient for creating and executing unit tests.

  Java

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated Oct 23, 2024Oct 23, 2024

• qPLEXanalyzer

  Public
  qPLEXanalyzer: Tools for qPLEX-RIME data analysis

  R

  •0•1•2•0•Updated Sep 18, 2024Sep 18, 2024

• pod5split

  Public
  Splitting tool for ONT Pod5 files

  Python

  •

  MIT License

  •1•0•0•0•Updated Sep 4, 2024Sep 4, 2024

• nf-rnaseq

  Public
  The Nextflow pipeline for quantifying RNAseq data using salmon

  Nextflow

  •

  BSD 2-Clause "Simplified" License

  •0•0•0•0•Updated Sep 2, 2024Sep 2, 2024

• rnaseqRcode

  Public
  R code for nf-rnaseq pipeline

  R

  •

  Other

  •0•0•0•0•Updated Sep 2, 2024Sep 2, 2024

• nf_trim_fastq

  Public
  Trims fastq files for adapter content etc. using fastp

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jul 29, 2024Jul 29, 2024

• struts-annotations

  Public
  Mirror of Apache Struts Annotations

  Java

  •8•0•0•0•Updated Jul 19, 2024Jul 19, 2024

• htsjdk-tools

  Public
  Command-line tools for processing high-throughput sequencing (HTS) data and genomic variants using the HTSJDK library.

  Java

  •

  MIT License

  •0•0•0•0•Updated Jun 4, 2024Jun 4, 2024

• shiny-base

  Public
  Base Docker image for Shiny applications

  Makefile

  •2•1•0•0•Updated Feb 2, 2024Feb 2, 2024

• shinystats

  Public
  Shiny app for one- and two-sample statistical tests

  R

  •

  MIT License

  •0•0•0•0•Updated Feb 2, 2024Feb 2, 2024

• GreyListChIP

  Public
  Bioconductor package: Grey Lists -- Mask Artefact Regions Based on ChIP Inputs

  R

  •0•1•0•0•Updated Dec 21, 2023Dec 21, 2023

• BamHeaderToRefflat

  Public
  Python

  •0•0•0•0•Updated Mar 9, 2023Mar 9, 2023

• PlateLayout

  Public
  Plate randomistation using R

  R

  •2•4•2•0•Updated Feb 27, 2023Feb 27, 2023

• mga-referencebuilder

  Public
  Java

  •0•0•0•0•Updated Jan 9, 2023Jan 9, 2023

• camcAPP

  Public
  shiny app to explore various prostate cancer datasets

  R

  •1•2•6•0•Updated Aug 12, 2022Aug 12, 2022

• bamMergeByScore

  Public
  Merge BAM files, keeping the best hit for each read

  Java

  •

  MIT License

  •1•0•0•0•Updated Mar 22, 2022Mar 22, 2022

• rascal

  Public
  R package and Shiny app providing functions for scaling relative copy number to absolute values for shallow whole genome sequencing of cancer samples.

  R

  •

  MIT License

  •4•12•1•0•Updated Oct 20, 2021Oct 20, 2021

• permCheck

  Public
  Report files and directories that do not follow permission rules.

  Ruby

  •

  MIT License

  •0•0•0•0•Updated Jun 11, 2021Jun 11, 2021

• redmine_common

  Public
  Common code for CRUK-CI Bioinformatics Core Redmine plugins

  JavaScript

  •

  GNU General Public License v3.0

  •0•0•0•0•Updated May 21, 2021May 21, 2021

• BCaPE

  Public
  R/Shiny app for Breast Cancer PDTX Encyclopaedia

  R

  •

  MIT License

  •1•1•0•0•Updated May 4, 2021May 4, 2021