Repositories list

• Platform

  Public
  place for documentation on how to run pipelines and guidelines for analysis

  HTML

  •

  MIT License

  •0•0•0•0•Updated Oct 31, 2024Oct 31, 2024

• rshiny_template

  Public template
  tempalte for any shiny from HCBC

  CSS

  •

  GNU General Public License v3.0

  •0•1•0•0•Updated Sep 12, 2024Sep 12, 2024

• scRNAseq_qc_app

  Public
  R

  •1•0•0•0•Updated Sep 12, 2024Sep 12, 2024

• bcbioSingleCell

  Public
  R package for bcbio single-cell RNA-seq analysis.

  R

  •

  GNU Affero General Public License v3.0

  •8•29•0•0•Updated Sep 9, 2024Sep 9, 2024

• bcbioRNASeq

  Public
  R package for bcbio RNA-seq analysis.

  R

  •

  GNU Affero General Public License v3.0

  •21•58•0•0•Updated Sep 9, 2024Sep 9, 2024

• bcbioBase

  Public
  Base functions for bcbio R packages.

  R

  •

  GNU Affero General Public License v3.0

  •3•2•0•0•Updated Sep 9, 2024Sep 9, 2024

• knowledgebase

  Public
  recipes that save time

  TeX

  •32•121•16•1•Updated Aug 30, 2024Aug 30, 2024

• tinyatlas

  Public
  A tiny cell atlas for commonly sequenced organisms.

  39•26•2•0•Updated Jul 9, 2024Jul 9, 2024

• hbc.github.io

  Public archive
  Jekyll based website for the Harvard Chan Bioinformatics Core

  SCSS

  •

  MIT License

  •906•3•0•0•Updated Jun 11, 2024Jun 11, 2024

• leafcutter

  Public
  Annotation-free quantification of RNA splicing. Yang I. Li, David A. Knowles, Jack Humphrey, Alvaro N. Barbeira, Scott P. Dickinson, Hae Kyung Im, Jonathan K. Pritchard

  R

  •

  Apache License 2.0

  •115•0•0•0•Updated Jun 1, 2024Jun 1, 2024

• HBC04813_Schatton_mouse_ATACseq

  Public
  R

  •0•1•0•0•Updated Apr 11, 2024Apr 11, 2024

• Molecular-convergence-between-Down-syndrome-and-Fragile-X-syndrome-hPSCs

  Public
  Code repository for the paper "Molecular convergence between Down syndrome and Fragile X syndrome identified using human pluripotent stem cell models"

  TeX

  •

  MIT License

  •1•1•0•0•Updated Aug 8, 2022Aug 8, 2022

• overmoyer2021_RNAseq_analysis_of_inflammatory_breast_cancer_hbc04141

  Public
  HTML

  •

  MIT License

  •1•1•0•0•Updated Jun 30, 2022Jun 30, 2022

• hbc_kim_ATACseq_BRG1_hbc04466

  Public
  ATACseq of BRG1

  HTML

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

• rowe2020_indrop_citeseq_hbc03948

  Public
  Shell

  •2•1•0•0•Updated Jan 18, 2022Jan 18, 2022

• tutorials

  Public
  This repo contains tutorials for different NGS analysis methods

  R

  •5•13•1•0•Updated Nov 29, 2021Nov 29, 2021

• hbc_timeseries_scRNAseq_lung_cancer_organoids_hbc03856

  Public
  HTML

  •0•0•0•0•Updated Nov 18, 2021Nov 18, 2021

• dou_ChIPseq_cytosolic_DNA_in_senescence_hbc04310

  Public
  Chip seq analysis of Cytoplasmic chromatin DNA

  0•0•0•0•Updated Oct 27, 2021Oct 27, 2021

• power_calc_simulations

  Public
  sample code for running simulation based power calculations

  0•0•0•0•Updated Jun 23, 2021Jun 23, 2021

• metabolomic_vizualization_manuscript

  Public
  0•0•0•0•Updated May 18, 2021May 18, 2021

• Clark_snRNA_seq_skin_biopsies_hbc04139-

  Public
  snRNA seq from CTCL skin sample OTC frozen

  Shell

  •0•0•0•0•Updated Feb 24, 2021Feb 24, 2021

• john_flanagan_insulin_receptor_chipseq_rnaseq

  Public
  Shell

  •1•0•0•0•Updated Jan 28, 2021Jan 28, 2021

• presentations

  Public
  0•0•0•0•Updated Sep 28, 2020Sep 28, 2020

• sequencing_guidelines

  Public
  0•0•0•0•Updated Apr 22, 2020Apr 22, 2020

• breakfast

  Public
  Details about the monthly breakfast hosted by the Harvard Chan Bioinformatics Core

  CSS

  •1•1•0•0•Updated Mar 10, 2020Mar 10, 2020

• A-single-cell-survey-of-Drosophila-blood

  Public
  TeX

  •

  MIT License

  •3•0•0•0•Updated Jan 27, 2020Jan 27, 2020

• drosophila-midgut-analysis

  Public
  Analysis scripts for 'A cell atlas of the adult drosophila midgut'

  HTML

  •3•3•0•0•Updated Dec 19, 2019Dec 19, 2019

• hbcABC

  Public
  Compilation of rmarkdown templates for bioinformatics analysis

  TeX

  •

  MIT License

  •3•5•1•0•Updated Sep 5, 2019Sep 5, 2019

• methods

  Public archive
  TeX

  •3•3•0•0•Updated Apr 16, 2019Apr 16, 2019

• MouseKidneyFibrOmics

  Public
  Repository with the analysis of two kidney fibrosis models in mouse

  proteinrshinygenes+ 2mirnafibrosis

  HTML

  •1•1•0•0•Updated Mar 13, 2019Mar 13, 2019