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    86 repositories

    • visutils

      Public
      set of function for qc and visualization of Visium data
      R
      •
      MIT License
      •0•1•0•0•Updated Oct 8, 2024Oct 8, 2024

    • schard

      Public
      reticulate-free single cell format conversion
      R
      •
      GNU General Public License v3.0
      •4•76•2•0•Updated Oct 8, 2024Oct 8, 2024

    • farmer

      Public
      Slack bot that tells you the status of your LSF jobs 🧑‍🌾
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Oct 8, 2024Oct 8, 2024

    • unwrap_CNS

      Public
      Truing visium spots of CNS from Embryo
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • image_registration_tools

      Public
      tools for image registration
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 7, 2024Oct 7, 2024

    • Image-ST

      Public
      A pipeline to generate count matrix for different spatial technologies. ISS/MERFISH-like data are decoded using PoSTcode
      Nextflow
      •
      MIT License
      •1•0•0•0•Updated Oct 5, 2024Oct 5, 2024

    • nf-irods-to-fastq

      Public
      Get CRAMs from iRODS and convert them to FASTQ
      Nextflow
      •
      MIT License
      •2•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • napari-large-3d-vis

      Public
      napari plugin which allows to visualize any size 3D volumetric image without exceeding maximum allowed RAM size
      Python
      •
      MIT License
      •0•0•0•0•Updated Oct 4, 2024Oct 4, 2024

    • GBM-stuff

      Public
      Storing the scripts for use in the GBM project
      Java
      •
      MIT License
      •0•1•1•0•Updated Oct 3, 2024Oct 3, 2024

    • dockage

      Public
      Cellgeni Docker files
      Dockerfile
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • fastapi_websocket_rpc

      Public
      ⚡ FASTAPI Websocket RPC- A fast and durable bidirectional JSON RPC channel over Websockets.
      Python
      •
      MIT License
      •24•1•0•0•Updated Sep 30, 2024Sep 30, 2024

    • cloupe

      Public
      Cloupe reader
      readersingle-cellloupe10x-genomics
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Sep 28, 2024Sep 28, 2024

    • reprocess_public_10x

      Public
      Scripts to help get fastqs
      Shell
      •
      GNU General Public License v3.0
      •3•12•1•0•Updated Sep 25, 2024Sep 25, 2024

    • STARsolo

      Public
      wrapper scripts for convenient STARsolo processing of 10X and other scRNA-seq
      Shell
      •
      GNU General Public License v3.0
      •5•44•0•0•Updated Sep 25, 2024Sep 25, 2024

    • visium2cells

      Public
      segmenting H&E images from Visium to assign each visium spot to the number of cell, occupancy and other morphological features of cells
      Python
      •
      MIT License
      •0•1•0•0•Updated Sep 24, 2024Sep 24, 2024

    • celltypist_census

      Public
      This repo includes the notebooks to test CellTypist by using the datasets downloaded from CELLxGENE portal by using Census.
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • nf-reprocessing-public-10x

      Public
      Nextflow pipeline of Alex's reprocessing scripts
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • alignment_HE_DAPI

      Public
      multimodal alignment H&E RGB images to DAPI one channel images
      Python
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • nf-starsolo

      Public
      Our STARsolo repo but designed for Nextflow Tower
      Shell
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • various_cellrangers

      Public
      Various Cellranger Scripts used for different version etc
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • cellxgene_curation

      Public
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • tracer-utils

      Public
      This repository contains scripts for running the Teichlab/tracer package.
      Shell
      •
      MIT License
      •0•0•0•0•Updated Sep 16, 2024Sep 16, 2024

    • nf-scautoqc

      Public
      Nextflow implementation of scAutoQC pipeline
      Python
      •
      GNU General Public License v3.0
      •0•1•0•0•Updated Sep 16, 2024Sep 16, 2024

    • cellranger_cite_hash

      Public
      Processing CITE-seq and cell hashing datasets with Cell Ranger
      Shell
      •
      GNU General Public License v3.0
      •0•2•0•0•Updated Sep 16, 2024Sep 16, 2024

    • nf-irods-to-fastq2

      Public
      0•0•0•0•Updated Sep 13, 2024Sep 13, 2024

    • nf-velocyto

      Public
      Our Velocyto repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • nf-cellbender

      Public
      Nextflow implementation of Cellbender
      R
      •
      MIT License
      •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • nf-demultiplex

      Public
      Our Souporcell repo but for Nextflow Tower
      Nextflow
      •
      MIT License
      •0•0•1•0•Updated Sep 12, 2024Sep 12, 2024

    • grnboost2-configuration

      Public archive
      Repository for storing general use configuration files for grnboost2
      Shell
      •
      MIT License
      •1•0•0•0•Updated Sep 12, 2024Sep 12, 2024

    • references

      Public
      MIT License
      •0•0•0•0•Updated Sep 12, 2024Sep 12, 2024