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    34 repositories

    • ACE

      Public
      R Shiny app for comparison of annotations (e.g., cell type assignments)
      R
      •
      Other
      •1•1•7•0•Updated Oct 19, 2024Oct 19, 2024

    • scrattch

      Public
      Single cell RNA-seq analysis for transcriptomic type characterization
      rumbrellatranscriptomicsscrattch
      R
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      Other
      •3•30•0•0•Updated Sep 13, 2024Sep 13, 2024

    • scrattch.mapping

      Public
      Genearlized mapping scripts for RNA-seq and Patch-seq data
      R
      •2•10•7•0•Updated Sep 13, 2024Sep 13, 2024

    • PeakRankR

      Public
      Package to rank enhancer peaks for cloning
      R
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      Other
      •0•0•0•0•Updated Sep 6, 2024Sep 6, 2024

    • EnhancerBenchmark

      Public
      R
      •0•2•0•0•Updated Aug 24, 2024Aug 24, 2024

    • scrattch.bigcat

      Public
      iterative clustering pipeline of big single cell datasets.
      R
      •10•24•4•2•Updated Aug 7, 2024Aug 7, 2024

    • mouse_aging_scRNAseq

      Public
      analysis scripts related to Jin et al manuscript on scRNA seq in aging mouse brain
      R
      •0•2•0•0•Updated Jun 14, 2024Jun 14, 2024

    • scrattch.vis

      Public
      scRNA-seq data visualization from scrattch
      rdata-visualizationtranscriptomicsscrattch
      R
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      Other
      •2•24•7•0•Updated Apr 10, 2024Apr 10, 2024

    • dLGN_cross_species

      Public
      R
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      Other
      •0•1•1•0•Updated Feb 13, 2024Feb 13, 2024

    • GeneOrthology

      Public
      CSV file and R package for collecting gene ortholog information from NCBI.
      R
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      Other
      •0•7•0•0•Updated Jan 16, 2024Jan 16, 2024

    • hodge2019data

      Public
      Subsetted single nucleus transcriptomic data from Hodge, et al. (2019)
      R
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      Other
      •0•0•0•0•Updated Oct 4, 2023Oct 4, 2023

    • QCR

      Public
      QCR stands for Quality Control workflow for sc/sn RNA-seq data
      R
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      Other
      •0•3•0•0•Updated Sep 29, 2023Sep 29, 2023

    • CERP

      Public
      R
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Jul 19, 2023Jul 19, 2023

    • CCN

      Public
      R library for applying Common Cell type Nomenclature (CCN) standard
      R
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      Other
      •1•2•1•0•Updated Apr 13, 2023Apr 13, 2023

    • ArchR

      Public
      ArchR : Analysis of Regulatory Chromatin in R (www.ArchRProject.com)
      R
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      MIT License
      •137•0•0•0•Updated Sep 27, 2022Sep 27, 2022

    • mapping

      Public
      R
      •0•0•0•0•Updated Aug 11, 2022Aug 11, 2022

    • L5_VEN

      Public
      This repository contains code for reproducing the analysis of snRNA-seq data from human fronto-insula
      R
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      Other
      •3•5•0•0•Updated Jul 27, 2022Jul 27, 2022

    • BarWare-manuscript

      Public
      R
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      Other
      •0•0•0•0•Updated Jan 26, 2022Jan 26, 2022

    • scrattch.io

      Public
      Functions for handling RNA-seq files and formats as input and output for scrattch functions.
      rhdf510xgenomicsloomtranscriptomicstome
      R
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      Other
      •3•11•10•1•Updated Nov 15, 2021Nov 15, 2021

    • BarMixer

      Public
      R
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      Other
      •1•2•0•0•Updated Oct 28, 2021Oct 28, 2021

    • aifi-swanson-teaseq

      Public
      Code related to Swanson, et. al. for TEA-seq, ICICLE-seq, and scATAC-seq data processing, analysis, and visualization
      atac-seqtea-seqicicle-seqscatac-seq
      R
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      Other
      •3•11•2•0•Updated Sep 20, 2021Sep 20, 2021

    • atlasplot

      Public
      Reproducible Plots for the Allen Institutes Brain Atlases
      R
      •
      GNU General Public License v2.0
      •1•1•0•0•Updated Aug 4, 2021Aug 4, 2021

    • agedbrain

      Public
      Code and files for reproducing the analysis presented in "Neuropathological and transcriptomic characteristics of the aged brain," the platform paper for the Aging, Dementia, and TBI Study.
      R
      •
      GNU General Public License v2.0
      •4•1•0•1•Updated Sep 8, 2020Sep 8, 2020

    • cocoframer

      Public
      COmmon COordinate FRAMEwork in R
      rccf3drgl
      R
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      Other
      •9•35•5•0•Updated May 19, 2020May 19, 2020

    • PeptidergicNetworks

      Public
      Repository for Smith et al. 2019
      R
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      MIT License
      •2•3•0•0•Updated Nov 19, 2019Nov 19, 2019

    • lowcat

      Public
      Low coverage accessibility and transcriptomics
      ratac-seqtranscriptomics
      R
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      Other
      •1•0•0•0•Updated Oct 7, 2019Oct 7, 2019

    • MTG_celltypes

      Public
      Human cortical cell types
      R
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      Other
      •7•24•1•0•Updated Aug 21, 2019Aug 21, 2019

    • tasic2016data

      Public
      Single cell transcriptomic data from Tasic, et al. (2016)
      transcriptomicsscrna-seq-datascrattch
      R
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      Other
      •0•9•0•0•Updated Jan 9, 2019Jan 9, 2019

    • tasic2018analysis

      Public
      Scripts related to VISp and ALM scRNA-seq and FISH analysis for Tasic, et al., 2018.
      R
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      Other
      •3•24•0•0•Updated Jun 15, 2018Jun 15, 2018

    • DevRhesusLMD

      Public
      Non-human primate brain development gene expression
      R
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      Other
      •8•0•0•0•Updated Nov 21, 2017Nov 21, 2017