hbc repositories

114 repositories

knowledgebase
Public
recipes that save time
R
•33•151•16•1•Updated Sep 18, 2026Sep 18, 2026
Platform
Public
place for documentation on how to run pipelines and guidelines for analysis
HTML
•
MIT License
•2•0•5•1•Updated Sep 14, 2026Sep 14, 2026
nextflow-editsqc
Public
Nextflow
•
MIT License
•0•0•0•0•Updated Aug 28, 2026Aug 28, 2026
nextflow-montgen
Public
braskem bacass version of the pipeline
Nextflow
•
MIT License
•0•0•3•0•Updated Jun 23, 2026Jun 23, 2026
app_mavrikaki_brain_aging_spatialtx_human_hbc05086
Public
vitessce
JavaScript
•
MIT License
•0•0•0•0•Updated Apr 22, 2026Apr 22, 2026
HBC04292_Hazra_RNA_exomecapture_human
Public
HTML
•0•0•0•0•Updated Nov 9, 2025Nov 9, 2025
HBC04855_Schatton_mouse_RNAseq
Public
HTML
•0•0•0•0•Updated Aug 14, 2025Aug 14, 2025
HBC04813_Schatton_mouse_ATACseq_extracode
Public
R
•1•0•0•0•Updated Jun 24, 2025Jun 24, 2025
HBC04813_Schatton_mouse_ATACseq
Public
R
•1•1•0•0•Updated Jun 24, 2025Jun 24, 2025
scRNAseq_qc_app
Public
R
•1•0•0•0•Updated Feb 13, 2025Feb 13, 2025
scrna_coexpression_workflow
Public
0•0•0•0•Updated Dec 9, 2024Dec 9, 2024
hbc_scRNA_merck_coexpression_of_genes_pilot_hbc04734
Public
R
•0•0•0•0•Updated Dec 9, 2024Dec 9, 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
bcbioSingleCell
Public
R package for bcbio single-cell RNA-seq analysis.
R
•
GNU Affero General Public License v3.0
•8•31•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•64•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
tinyatlas
Public
A tiny cell atlas for commonly sequenced organisms.
38•30•2•1•Updated Jul 9, 2024Jul 9, 2024
hbc.github.io
Public archive
Jekyll based website for the Harvard Chan Bioinformatics Core
SCSS
•
MIT License
•876•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. P…
R
•
Apache License 2.0
•122•0•0•0•Updated Jun 1, 2024Jun 1, 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
•4•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

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Harvard Chan School: Bioinformatics Core

All

114 repositories

knowledgebase

Platform

nextflow-editsqc

nextflow-montgen

app_mavrikaki_brain_aging_spatialtx_human_hbc05086

HBC04292_Hazra_RNA_exomecapture_human

HBC04855_Schatton_mouse_RNAseq

HBC04813_Schatton_mouse_ATACseq_extracode

HBC04813_Schatton_mouse_ATACseq

scRNAseq_qc_app

scrna_coexpression_workflow

hbc_scRNA_merck_coexpression_of_genes_pilot_hbc04734

rshiny_template

bcbioSingleCell

bcbioRNASeq

bcbioBase

tinyatlas

hbc.github.io

leafcutter

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

overmoyer2021_RNAseq_analysis_of_inflammatory_breast_cancer_hbc04141

hbc_kim_ATACseq_BRG1_hbc04466

rowe2020_indrop_citeseq_hbc03948

tutorials

hbc_timeseries_scRNAseq_lung_cancer_organoids_hbc03856

dou_ChIPseq_cytosolic_DNA_in_senescence_hbc04310

power_calc_simulations

metabolomic_vizualization_manuscript

Clark_snRNA_seq_skin_biopsies_hbc04139-

john_flanagan_insulin_receptor_chipseq_rnaseq

Repositories list

114 repositories