Repositories list

• spatial_hpc

  Public
  Repository for the spatial (U01) hippocampus (hipc) project

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  •0•1•1•0•Updated Nov 22, 2024Nov 22, 2024

• globus

  Public
  LIBD Globus Share Endpoints

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  •1•0•0•0•Updated Nov 19, 2024Nov 19, 2024

• visiumStitched_brain

  Public
  Example human brain data used for https://research.libd.org/visiumStitched/.

  spatialrstatsbioconductor+ 4transcriptomicsvisiumspatiallibdvisiumstitched

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  •0•0•0•0•Updated Nov 8, 2024Nov 8, 2024

• ls_molecular-profiling

  Public
  ls_molecular-profiling

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  •0•1•0•0•Updated Sep 25, 2024Sep 25, 2024

• spatial_DG_lifespan

  Public
  Spatial transcriptomics (Visium) in dentate gyrus of hippocampus over the lifespan

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  •0•0•0•0•Updated Sep 20, 2024Sep 20, 2024

• goesHyde_mdd_rnaseq

  Public
  Fernando Goes and Thomas Hyde MDD RNA-seq project

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  •0•1•7•0•Updated Aug 27, 2024Aug 27, 2024

• DLPFC_snRNAseq

  Public
  snRNA_seq portion of the spatialDLPFC project

  rstatsbioconductorsnrna-seq+ 1spatialdlpfc

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  •1•5•0•0•Updated Aug 16, 2024Aug 16, 2024

• zandiHyde_bipolar_rnaseq

  Public
  RNA-seq analysis for psychENCODE R01

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  •1•6•0•0•Updated Aug 15, 2024Aug 15, 2024

• deconvo_lute-paper

  Public
  Contains analysis for the lute software paper

  rneurosciencebioconductor+ 2transcriptomicsdeconvolution

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  MIT License

  •0•1•0•0•Updated Aug 5, 2024Aug 5, 2024

• Habenula_Pilot

  Public
  habenulaPilot project code repository

  rna-seqschizophreniabulk-rna-seq+ 2snrna-seqhabenula

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  •0•0•2•0•Updated Jul 11, 2024Jul 11, 2024

• HumanPilot

  Public
  Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project

  analysishumanrstats+ 6biorxivbrain10xgenomicsspatial-transcriptomicsvisiumdlpfc

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  •29•71•0•0•Updated May 24, 2024May 24, 2024

• spatialDLPFC

  Public
  spatialDLPFC project involving Visium (n = 30), Visium SPG (n = 4) and snRNA-seq (n = 19) samples

  rstatsbioconductortranscriptomics+ 5spatial-transcriptomicsvisiumdlpfcspatialdlpfcvisium-spg

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  •3•17•1•0•Updated May 22, 2024May 22, 2024

• Visium_SPG_AD

  Public
  Visium SPG AD project (n = 10) using Visium Spatial Proteogenomics (Visium-SPG) on dissections from the inferior temporal cortex (ITC) from Alzheimer's disease cases and controls.

  rstatsbioconductortranscriptomics+ 5alzheimers-diseasespatial-transcriptomicsvisiumvisium-spgvisium-spg-ad

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  •0•3•2•0•Updated May 8, 2024May 8, 2024

• SPEAQeasy

  Public
  SPEAQeasy: portable LIBD RNA-seq pipeline using Nextflow. Check http://research.libd.org/SPEAQeasy-example/ for an example on how to use this pipeline and analyze the resulting output files.

  pipelinerstatsrnaseq+ 4hisat2speaqeasynextflowrna-seq-pipeline

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  MIT License

  •4•6•21•0•Updated Jan 26, 2024Jan 26, 2024

• brainseq_phase2

  Public
  BrainSeq Phase II project lead by LIBD for the BrainSeq Consortium

  rstatsrnaseqschizophrenia+ 3brainseqphase2sczdbrainseq

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  •5•8•0•0•Updated Jan 7, 2024Jan 7, 2024

• septum_lateral

  Public
  10x-based sequencing in the lateral septum (mouse & human)

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  •0•0•4•0•Updated Nov 17, 2023Nov 17, 2023

• BiocMAP

  Public
  Our typical analysis steps for WGBS data, starting from FASTQ reads and ending with the construction of bsseq objects. Created using nextflow

  nextflowwgbs

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  •0•2•4•0•Updated Sep 15, 2023Sep 15, 2023

• 10xPilot_snRNAseq-human

  Public
  10x snRNA-seq study on 5 postmortem human brain regions across the reward circuitry: NAc, AMY, sACC, DLPFC, and HPC

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  •9•21•0•0•Updated Jul 15, 2022Jul 15, 2022

• qsva_brain

  Public
  qSVA adapted for 2 brain regions as part of the BrainSeq Phase II project

  rstatsrnaseqschizophrenia+ 3degradationbrainseqphase2sczd

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  •0•2•0•0•Updated Mar 4, 2022Mar 4, 2022

• libd_stem_timecourse

  Public
  rnaseqcellstem+ 1timecourse

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  MIT License

  •0•6•0•0•Updated May 27, 2021May 27, 2021

• recount-brain

  Public
  Code and analyses for the recount-brain project

  metadatapublichuman+ 3rstatsrnaseqrecount

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  MIT License

  •2•8•1•0•Updated Nov 13, 2020Nov 13, 2020

• jaffe_onboarding

  Public
  Jaffe lab onboarding materials

  websiterstatsonbording

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  •0•1•0•0•Updated Jan 13, 2020Jan 13, 2020

• miRNA_Kit_Comparison

  Public
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  MIT License

  •1•1•0•0•Updated Aug 23, 2019Aug 23, 2019

• recountWorkshop

  Public
  Package for the recount workshop for BioC2017

  countgener+ 11humanrstatsbioconductorrnaseqdeseq2illuminaexon+ 4

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  •1•1•0•0•Updated Aug 23, 2019Aug 23, 2019

• insp

  Public
  Collaboration with INSP researcher Jesus Martinez using recount data

  recount

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  •0•0•0•0•Updated Jan 14, 2019Jan 14, 2019

• as3mt-paper

  Public
  Data and code from Ming et al, Nature Medicine, 2016 on dissecting GWAS signal from the 10q24.32 region

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  •0•0•0•0•Updated Mar 29, 2016Mar 29, 2016