Repositories list

• nf-omicstd

  Public
  Nextflow for rnaseq workflow

  Jupyter Notebook

  •0•0•0•0•Updated Sep 27, 2024Sep 27, 2024

• checkatlas

  Public
  One liner tool to check the quality of your single-cell atlases.

  qualitycontrolmultiqc+ 4single-cellseuratscanpypython

  HTML

  •

  BSD 3-Clause "New" or "Revised" License

  •1•3•16•0•Updated Apr 10, 2024Apr 10, 2024

• nf-blast

  Public
  Nextflow - Blast workflow

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Nov 20, 2023Nov 20, 2023

• MultiQC

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

  Python

  •

  GNU General Public License v3.0

  •603•0•0•0•Updated Jul 25, 2023Jul 25, 2023

• nf-core-checkatlas

  Public
  One liner tool to check the quality of your single-cell atlases.

  Nextflow

  •

  MIT License

  •0•0•0•0•Updated Jul 25, 2023Jul 25, 2023

• MultiQC_TestData

  Public
  Test data for MultiQC. See https://github.com/ewels/MultiQC

  HTML

  •

  MIT License

  •145•0•0•0•Updated Jul 21, 2023Jul 21, 2023

• scCellMarkers

  Public
  Website for screening marker genes to lung cell type hierarchical graph

  Python

  •

  Apache License 2.0

  •1•0•0•0•Updated Jun 12, 2023Jun 12, 2023

• BioRegul

  Public
  Apache License 2.0

  •0•0•0•0•Updated Jun 6, 2023Jun 6, 2023

• bacnet

  Public
  BACNET is a Java based platform to develop website for multi-omics analysis

  websitebioinformaticsgenomics+ 6data-visualizationproteomicstranscriptomicsbacnetmulti-omicslisteria

  Java

  •

  GNU General Public License v3.0

  •1•13•24•0•Updated Feb 21, 2023Feb 21, 2023

• cellranger-to-scanpy

  Public
  A small python script to import cellranger analysis into Scapy. It loads scRNA-Seq experiment out of cellranger, includes the count matrices, the UMAP+T-SNE reduction, the clustering, and normalized RNA count matrix.

  Python

  •

  MIT License

  •0•1•0•0•Updated Jul 27, 2022Jul 27, 2022

• rap-e4-war-export

  Public
  An example eclipse RAP e4 project which can be export to .war file

  Java

  •

  MIT License

  •1•0•0•0•Updated Dec 20, 2021Dec 20, 2021

• cellranger-to-seurat

  Public
  A small R script to import cellranger analysis into Seurat. It includes the count matrices, the UMAP+T-SNE reduction, and the clustering

  R

  •

  MIT License

  •0•0•0•0•Updated Jun 17, 2021Jun 17, 2021

• ListeriomicsSample

  Public
  Sample dataset used for starting up BACNET demo

  Shell

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated May 18, 2020May 18, 2020

• HCA_analysis

  Public
  An atlas of the healthy airway epithelium -

  HTML

  •2•0•0•0•Updated Feb 13, 2020Feb 13, 2020

• scATAC-benchmarking

  Public
  Benchmarking computational single cell ATAC-seq methods

  Jupyter Notebook

  •

  MIT License

  •39•0•0•0•Updated Dec 5, 2019Dec 5, 2019

• RIPSeq-Listeria

  Public
  RIP-Seq and RNA-Seq of an RNA-binding protein secreted by Listeria monocytogenes which activates RIG-I signaling Secreted bacterial

  R

  •

  GNU General Public License v3.0

  •2•1•0•0•Updated Nov 28, 2019Nov 28, 2019

• seurat

  Public
  R toolkit for single cell genomics

  R

  •

  GNU General Public License v3.0

  •917•0•0•0•Updated Oct 9, 2019Oct 9, 2019

• signac

  Public
  R toolkit for the analysis of single-cell chromatin data

  R

  •

  Other

  •88•0•0•0•Updated Aug 30, 2019Aug 30, 2019

• biojava

  Public
  📖🔬☕ BioJava is an open-source project dedicated to providing a Java library for processing biological data.

  Java

  •

  GNU Lesser General Public License v2.1

  •388•0•0•0•Updated Jun 23, 2019Jun 23, 2019

• MeRIPSeq

  Public
  MeRIP-Seq pipeline analysis for m6a methylation site detection

  Python

  •

  GNU General Public License v3.0

  •0•6•0•0•Updated Jun 12, 2019Jun 12, 2019