Brickman Lab
Professor Joshua Brickman at Center for Stem Cell Medicine (reNEW), University of Copenhagen
Copenhagen
Pinned Repositories
adv_scrnaseq_2020
Material for lectures and exercises of the SIB course "Advanced topics in single-cell transcriptomics" (May 2020)
ALPS
AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project
brickmanlab.github.io
Brickman Lab (wiki)
commonR
Common R functions and pipelines for Brickman Lab
custom-containers
Custom Docker images
marsseq
MARS-seq v2 pre-processing pipeline with velocity
ngs-template
preimplantation-portal
https://brickman-preimplantation.streamlit.app
proks-salehin-et-al
Deep Learning Based Models for Preimplantation Mouse and Human Development
rothova-et-al-2022
Brickman Lab's Repositories
brickmanlab/commonR
Common R functions and pipelines for Brickman Lab
brickmanlab/rothova-et-al-2022
brickmanlab/custom-containers
Custom Docker images
brickmanlab/proks-salehin-et-al
Deep Learning Based Models for Preimplantation Mouse and Human Development
brickmanlab/ALPS
AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project
brickmanlab/brickmanlab.github.io
Brickman Lab (wiki)
brickmanlab/CAT
Cluster Alignment Tool (CAT)
brickmanlab/marsseq
MARS-seq v2 pre-processing pipeline with velocity
brickmanlab/ngs-template
brickmanlab/preimplantation-portal
https://brickman-preimplantation.streamlit.app
brickmanlab/.github
reNEW Brickman Group
brickmanlab/10X
10X helper scripts with velocity estimation
brickmanlab/Beeline
BEELINE: evaluation of algorithms for gene regulatory network inference
brickmanlab/CRISPRiScreen
Analysis pipeline to identify enhancer-target gene interactions from TAP-seq or Perturb-seq experiments.
brickmanlab/cutandrun
Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
brickmanlab/knudsen_et_al_2022
brickmanlab/linneberg-agerholm-et-al-2023
brickmanlab/manuscript-templates
LaTeX templates for manuscripts. bioRxiv preprint and journal submission templates. For use on Overleaf.
brickmanlab/mars-seq2-inhouse
brickmanlab/morganti-et-al-2023
brickmanlab/nf-co.re
Code and files for the main nf-core website.
brickmanlab/perera_et_al_2022
Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming
brickmanlab/project-template
Cokkiecutter R/Python project template
brickmanlab/proks-et-al-2023
brickmanlab/riveiro-et-al-2023
brickmanlab/RTemplates
brickmanlab/scrnaseq
A single-cell RNAseq pipeline for 10X genomics data
brickmanlab/scRNAviz
brickmanlab/TAPseq_workflow
A Snakemake workflow for TAP-seq data processing
brickmanlab/wong-et-al-2022