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    33 repositories

    • brickmanlab.github.io

      Public
      Brickman Lab (wiki)
      Creative Commons Attribution Share Alike 4.0 International
      •0•1•0•0•Updated Oct 3, 2024Oct 3, 2024

    • scanvi-explainer

      Public
      scANVI Explainer
      shapscvi-tools
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 30, 2024Sep 30, 2024

    • cat-python

      Public
      Cluster Alignment Tool (CAT)
      distancescrna-seq
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 17, 2024Sep 17, 2024

    • preimplantation-portal

      Public
      https://brickman-preimplantation.streamlit.app
      Jupyter Notebook
      •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • primeseq

      Public
      PRIME-seq preprocessing nf-core pipeline
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Aug 2, 2024Aug 2, 2024

    • ngs-template

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jul 30, 2024Jul 30, 2024

    • scrnaseq

      Public
      A single-cell RNAseq pipeline for 10X genomics data
      Nextflow
      •
      MIT License
      •167•0•0•0•Updated Jun 7, 2024Jun 7, 2024

    • Beeline

      Public
      BEELINE: evaluation of algorithms for gene regulatory network inference
      Python
      •
      GNU General Public License v3.0
      •53•0•0•0•Updated May 29, 2024May 29, 2024

    • linneberg-agerholm-et-al-2024

      Public
      The primitive endoderm supports lineage plasticity to enable regulative development
      Jupyter Notebook
      •0•0•0•0•Updated May 21, 2024May 21, 2024

    • proks-salehin-et-al

      Public
      Deep Learning Based Models for Preimplantation Mouse and Human Development
      bioinformaticsdevelopmental-biologyshapley-valuescvi-tools
      Jupyter Notebook
      •0•1•0•0•Updated May 10, 2024May 10, 2024

    • manuscript-templates

      Public
      LaTeX templates for manuscripts. bioRxiv preprint and journal submission templates. For use on Overleaf.
      TeX
      •
      GNU General Public License v3.0
      •39•0•0•0•Updated Apr 21, 2024Apr 21, 2024

    • riveiro-et-al-2023

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Dec 5, 2023Dec 5, 2023

    • cutandrun

      Public
      Analysis pipeline for CUT&RUN and CUT&TAG experiments that includes QC, support for spike-ins, IgG controls, peak calling and downstream analysis.
      Nextflow
      •
      MIT License
      •46•0•0•0•Updated Sep 27, 2023Sep 27, 2023

    • CRISPRiScreen

      Public
      Analysis pipeline to identify enhancer-target gene interactions from TAP-seq or Perturb-seq experiments.
      R
      •2•0•0•0•Updated Aug 29, 2023Aug 29, 2023

    • knudsen_et_al_2022

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jul 6, 2023Jul 6, 2023

    • TAPseq_workflow

      Public
      A Snakemake workflow for TAP-seq data processing
      Python
      •
      MIT License
      •4•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • nf-co.re

      Public
      Code and files for the main nf-core website.
      PHP
      •
      MIT License
      •189•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • proks-et-al-2023

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Jun 30, 2023Jun 30, 2023

    • marsseq

      Public
      MARS-seq v2 pre-processing pipeline with velocity
      Nextflow
      •
      MIT License
      •3•0•0•0•Updated Jun 6, 2023Jun 6, 2023

    • project-template

      Public archive
      Cokkiecutter R/Python project template
      GNU General Public License v3.0
      •0•0•0•0•Updated May 14, 2023May 14, 2023

    • .github

      Public
      reNEW Brickman Group
      0•0•0•0•Updated May 9, 2023May 9, 2023

    • ALPS

      Public
      AnaLysis routines for ePigenomicS data - 🏫 Bioconductor project
      R
      •
      Other
      •3•0•0•0•Updated Mar 2, 2023Mar 2, 2023

    • morganti-et-al-2023

      Public
      0•0•0•0•Updated Jan 26, 2023Jan 26, 2023

    • wong-et-al-2022

      Public
      HTML
      •0•1•0•0•Updated Nov 17, 2022Nov 17, 2022

    • perera_et_al_2022

      Public
      Transcriptional heterogeneity and cell cycle regulation as central determinants of primitive endoderm priming
      HTML
      •0•0•0•0•Updated Aug 1, 2022Aug 1, 2022

    • rothova-et-al-2022

      Public
      Jupyter Notebook
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated May 20, 2022May 20, 2022

    • 10X

      Public
      10X helper scripts with velocity estimation
      Shell
      •0•0•0•0•Updated Jan 17, 2022Jan 17, 2022

    • commonR

      Public
      Common R functions and pipelines for Brickman Lab
      R
      •
      Apache License 2.0
      •0•2•1•0•Updated Dec 14, 2021Dec 14, 2021

    • scRNAviz

      Public
      R
      •
      Apache License 2.0
      •0•0•0•0•Updated Aug 10, 2021Aug 10, 2021

    • custom-containers

      Public
      Custom Docker images
      Dockerfile
      •0•1•0•0•Updated May 25, 2021May 25, 2021