Repositories list

• data-management-python

  Public
  Python library for running data analysis pipelines for IGF team

  mysqlpythonsqlalchemy+ 3ngspandasillumina

  Python

  •

  Apache License 2.0

  •2•4•0•4•Updated Sep 9, 2024Sep 9, 2024

• igf-dockerfiles

  Public
  A list of dockerfiles for Docker and singularity image building

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

• IGF-aws-terraform

  Public
  A repository for storing terraform configs

  HCL

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

• igf-airflow-hpc

  Public
  Airflow dags and scripts for HPC

  Python

  •

  Apache License 2.0

  •0•3•0•0•Updated Jul 16, 2024Jul 16, 2024

• IGFPortal

  Public
  HTML

  •

  Apache License 2.0

  •0•0•0•4•Updated May 27, 2024May 27, 2024

• igf-pipeline-help

  Public
  A repository for keeping help documentation of IGF pipelines

  HTML

  •

  Apache License 2.0

  •1•1•0•0•Updated Mar 13, 2024Mar 13, 2024

• scanpy-notebook-image

  Public
  A repository for keeping conda env and docker image file for running single cell analysis using scanpy

  Jupyter Notebook

  •

  Apache License 2.0

  •3•5•0•0•Updated Mar 6, 2024Mar 6, 2024

• demultiplexing_report

  Public
  A repository for storing codes for de-multiplexing report generaltion

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 29, 2023Nov 29, 2023

• pipeline_tutorial_notebooks

  Public
  Jupyter notebook based tutorial for Nextflow

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Nov 27, 2023Nov 27, 2023

• igf-analysis

  Public
  A repository for storing analysis scripts

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 6, 2022Aug 6, 2022

• Metadata_validation

  Public archive
  A flask based metadata validation server

  Python

  •

  Apache License 2.0

  •0•0•0•7•Updated Jun 22, 2022Jun 22, 2022

• interop-notebook-image

  Public
  A repository for keeping notebooks for Interop data processing

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Apr 14, 2022Apr 14, 2022

• seurat-notebook-image

  Public
  A repository for keeping conda env and docker image file for running single cell analysis using Seurat

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 29, 2021Oct 29, 2021

• scirpy-notebook-image

  Public
  A repository for keeping conda env and docker image file for running single cell analysis using scirpy

  Jupyter Notebook

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 29, 2021Oct 29, 2021

• rnaseq-notebook-image

  Public
  A repository for keeping conda env and docker image file for running RNA-Seq analysis

  Dockerfile

  •

  Apache License 2.0

  •1•0•0•0•Updated Oct 7, 2021Oct 7, 2021

• base-notebook-image

  Public
  A repository for keeping conda env and docker files for the base notebook container image

  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Oct 6, 2021Oct 6, 2021

• LimsMetadataParsing

  Public
  A pyspark based codebase for fetching and formatting metadata from a LIMS db for IGF

  apache-sparkpandaspython-3-6+ 3sparksqlpyodbcapache-arrow

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jul 22, 2021Jul 22, 2021

• spark-notebook-image

  Public archive
  A repository for running Apache Spark via Jupyter notebook

  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 7, 2021Jun 7, 2021

• hail-notebook-image

  Public archive
  A repository for keeping conda env and docker image file for running single cell analysis using Hail.is

  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Feb 3, 2021Feb 3, 2021

• viral-genome-notebook-image

  Public archive
  A repo for keeping notebooks for viral genome analysis and data visualization

  Dockerfile

  •

  Apache License 2.0

  •1•0•0•0•Updated Dec 3, 2020Dec 3, 2020

• igf-airflow-scripts

  Public
  A repository for keeping scripts for running Apache Airflow based pipeline for IGF

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Sep 27, 2020Sep 27, 2020

• sample_tracking_database

  Public archive
  A database for tracking sample information in the lab

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Aug 2, 2020Aug 2, 2020

• igftools-kube-deploy

  Public archive
  IGFtools server deployment using Kubernetes

  Apache License 2.0

  •0•0•0•0•Updated Mar 26, 2020Mar 26, 2020

• Metadata_validation_docker

  Public archive
  A docker file for metadata validation server

  Dockerfile

  •

  Apache License 2.0

  •1•0•0•0•Updated Mar 25, 2020Mar 25, 2020

• igf-pipelines

  Public archive
  A repository of pipelines and scripts for Imperial BRC Genomics Facility team

  Perl

  •

  Apache License 2.0

  •0•1•0•0•Updated Jan 28, 2020Jan 28, 2020

• singlecell-notebooks-image

  Public archive
  A repository for storing conda env and docker image file for running single cell analysis

  Dockerfile

  •

  Apache License 2.0

  •0•0•0•0•Updated Dec 18, 2019Dec 18, 2019

• IlluminaDemultiplexingReportSpark

  Public
  A repository for generating de-multiplexing report for Illumina sequencing runs using Pyspark

  apache-sparkjinja2illumina+ 1demultiplexing

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 30, 2019Jun 30, 2019

• igf-basespace

  Public
  A repository for keeping Illumina Basespace specific codes for IGF team

  Python

  •

  Apache License 2.0

  •0•0•0•0•Updated Jun 27, 2019Jun 27, 2019

• imperial-genomics-facility.github.io

  Public
  Imperial Genomics Facility Git Hub Pages

  HTML

  •

  Creative Commons Zero v1.0 Universal

  •0•0•0•0•Updated May 15, 2019May 15, 2019

• internal-dashboard

  Public archive
  TypeScript

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