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@cancerbits Developmental Cancer Genomics

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    22 repositories

    • cancerbits.github.io

      Public
      Lab website.
      bioinformaticsgenomicscancercomputational-biologycancer-genomicsdevelopmental-biologystem-cell-differentiation
      HTML
      •0•0•0•0•Updated Dec 9, 2024Dec 9, 2024

    • ransmayr2024_ltbr

      Public
      Code used for the analysis of single-cell RNA-seq data presented in Ransmayr et al., 2024
      R
      •0•0•0•0•Updated Nov 26, 2024Nov 26, 2024

    • ressler2024_neobcc

      Public
      HTML
      •0•1•0•0•Updated Sep 11, 2024Sep 11, 2024

    • conveRtainer

      Public
      Docker containers + scripts for file conversions.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Apr 24, 2024Apr 24, 2024

    • saldana_montano2024_ncnb

      Public
      Code repository accompanying the paper by Saldana & Montano et al. (2024), Nat. Commun.
      R
      •0•0•0•0•Updated Mar 28, 2024Mar 28, 2024

    • scDE_benchmark

      Public
      Benchmark study for single-cell single-sample differential expression pipelines
      R
      •0•2•0•0•Updated Mar 27, 2024Mar 27, 2024

    • Kirchberger_Shoeb2024_neut

      Public
      Code repository accompanying the paper by Kirchberger, Shoeb, et al. (2024), Nat. Commun.
      Dockerfile
      •0•0•0•0•Updated Feb 28, 2024Feb 28, 2024

    • cellxgene_data_examples

      Public
      1•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • vitessce_data_examples

      Public
      Examples and instructions for configuring vitessce for Seurat objects.
      1•0•0•0•Updated Feb 23, 2024Feb 23, 2024

    • DElegate

      Public
      Wrapper and helper functions to use bulk RNA-seq differential expression methods with single-cell data
      R
      •
      GNU General Public License v3.0
      •3•17•3•0•Updated Feb 4, 2024Feb 4, 2024

    • kostelbal2023_nfatc1

      Public archive
      R code used for the analysis of single-cell RNA-seq data presented in Köstel Bal et al., Blood, 2023
      R
      •0•0•0•0•Updated May 30, 2023May 30, 2023

    • .github

      Public
      0•0•0•0•Updated Dec 22, 2022Dec 22, 2022

    • canceRbits

      Public
      Wrapper and helper functions commonly used by the Developmental Cancer Genomics group at St. Anna Children's Cancer Research Institute
      R
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Oct 18, 2022Oct 18, 2022

    • shahin2021_ikzf2_het

      Public archive
      Code repository accompanying the paper by Shahin et al. (2021), Blood Adv
      bioinformaticsscrna-seqimmunologyrare-disease
      R
      •
      MIT License
      •0•0•0•0•Updated Jan 28, 2022Jan 28, 2022

    • shahin2021_ikzf2

      Public archive
      Code repository accompanying the paper by Shahin et al. (2021), Sci. Immunol.
      bioinformaticsscrna-seqimmunologyrare-disease
      R
      •0•0•0•0•Updated Nov 26, 2021Nov 26, 2021

    • santini2021_imprints

      Public archive
      Code repository accompanying the paper by Santini, Halbritter, et al. (2021), Nat. Commun.
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

    • agerer2021_covid_epitopes

      Public archive
      Code repository accompanying the paper by Agerer et al. (2021), Sci. Immunol.
      bioinformaticscovid-19sars-cov-2
      R
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 16, 2021Sep 16, 2021

    • lch_hierarchy

      Public archive
      Code for Epigenomics and Single-cell Sequencing Define a Developmental Hierarchy in Langerhans Cell Histiocytosis (Halbritter, Farlik, et al. 2019 Cancer Discov.)
      R
      •3•0•0•0•Updated Mar 3, 2020Mar 3, 2020

    • nucpipe

      Public
      Python
      •2•0•0•0•Updated Nov 9, 2019Nov 9, 2019

    • SLICE

      Public
      A method for calculating single cell entropy and reconstructing cell differentiation lineage using single-cell RNA-seq data
      R
      •8•0•0•0•Updated Mar 14, 2019Mar 14, 2019

    • cnn_graph

      Public
      Convolutional Neural Networks on Graphs with Fast Localized Spectral Filtering
      Jupyter Notebook
      •
      MIT License
      •390•0•0•0•Updated Feb 13, 2019Feb 13, 2019

    • keras-gcn

      Public
      Keras implementation of Graph Convolutional Networks
      Python
      •
      MIT License
      •266•0•0•0•Updated Feb 6, 2019Feb 6, 2019