Repositories list

• plot_pe_mapping_status_from_bam

  Public
  From a single bam, plot coverage considering mate, pe mapping status and strand.

  R

  •0•0•0•0•Updated Nov 18, 2024Nov 18, 2024

• sav_call

  Public
  Stand-aware Variant caller

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• fctBio

  Public
  R package with objects and methods for functional biology analysis

  r-package

  R

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• terraform_nf_awsbatch

  Public
  awsnextflowterraform

  HCL

  •

  Apache License 2.0

  •0•0•1•0•Updated Nov 4, 2024Nov 4, 2024

• tf-single-ec2

  Public
  a terraform template to popup a single ec2

  awsterraform

  HCL

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• viral-variant

  Public
  Calling variants (exhaustive - by position) with peptide impact and comparison between samples (via transfer annotation)

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• nf-process

  Public
  Process as modules

  nextflownextflow-modules

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 28, 2024Oct 28, 2024

• viral-assembly

  Public
  Assemble the viral genome and perform the associated quality control (QC). Start with raw reads and one pre-built reference database in standard format (see README.md).

  nextflownextflow-pipeline

  Nextflow

  •

  Apache License 2.0

  •0•0•1•0•Updated Oct 25, 2024Oct 25, 2024

• nf-subworkflows

  Public
  subworkflows for nextflow

  nextflownextflow-modules

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 25, 2024Oct 25, 2024

• ghcr-pandas

  Public
  Python with pandas

  container-image

  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• spawn-rstudio

  Public
  Script to spawn locally a rstudio server

  rstudiospawner

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• hannot

  Public
  nextflow pipeline for annotation using homology

  nextflownextflow-pipeline

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 15, 2024Oct 15, 2024

• genvar

  Public
  Python

  •0•0•0•0•Updated Oct 14, 2024Oct 14, 2024

• ghcr-ivar

  Public
  Dockerfile

  •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

• loose_ends

  Public
  Get rid of base at reads ends in a pileup file

  C++

  •0•0•0•0•Updated Oct 11, 2024Oct 11, 2024

• primary

  Public
  Primary is a pipeline dedicated for all sequences to be processed for primary analysis.

  nextflownextflow-pipeline

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

• ghcr-py-bioseq

  Public
  Python for bioinformatic NGS analysis including biopython, pysam, h5py and others.

  Dockerfile

  •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

• compress_fq

  Public
  Workflow to compress a whole directory from fastq files to spring with sequence check.

  nextflownextflow-pipeline

  Nextflow

  •0•0•1•0•Updated Oct 3, 2024Oct 3, 2024

• tf_tk

  Public
  terrform toolkit

  terraformterraform-module

  HCL

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 24, 2024Sep 24, 2024

• ghcr-spades

  Public
  Docker image definition for the spades software

  Dockerfile

  •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

• nf-config

  Public
  config files for nextflow

  nextflownextflow-modules

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

• db-kraken2-custom

  Public
  Build kraken2 custom database

  database

  Shell

  •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

• nf-template

  Public template
  Template for nextflow project

  nextflowtemplate-projectnextflow-modules

  Nextflow

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

• ghcr-kraken2

  Public
  kraken2

  container-image

  Dockerfile

  •0•0•0•0•Updated Aug 23, 2024Aug 23, 2024

• ghcr-r-nexoverse

  Public
  r docker image with the nexoverse, a list of packages used often at Nexomis

  container-image

  R

  •0•0•1•0•Updated Aug 9, 2024Aug 9, 2024

• ghcr-r

  Public
  base r docker image

  container-image

  Dockerfile

  •0•0•0•0•Updated Aug 9, 2024Aug 9, 2024

• rna-preprocessing

  Public
  Estimate the expression level of features (genes or transcripts) and perform the associated QC. Starting from cleaned reads and one pre-built reference database in standard format (cf. Readme.md).

  nextflownextflow-pipeline

  Nextflow

  •

  Apache License 2.0

  •0•0•1•0•Updated Jul 2, 2024Jul 2, 2024

• nexodiff

  Public
  Nexomis package to establish RNA-seq differential signatures

  r-package

  R

  •

  Apache License 2.0

  •0•0•1•0•Updated Jun 16, 2024Jun 16, 2024

• viral_comp

  Public
  nextflownextflow-pipeline

  Python

  •0•0•0•0•Updated May 28, 2024May 28, 2024

• ghcr-spring

  Public
  docker image for https://github.com/shubhamchandak94/Spring

  container-image

  Dockerfile

  •0•0•0•0•Updated May 28, 2024May 28, 2024