Repositories list

• Lee_2023

  Public
  All the code described in the Lee et al. (2023) paper

  Jupyter Notebook

  •5•6•6•0•Updated Sep 17, 2024Sep 17, 2024

• multi_padlock_design

  Public
  Padlock design pipeline for multiplexed assay with multiple probes per target in cDNA-based expression profiling

  Python

  •

  MIT License

  •13•13•7•0•Updated Jul 11, 2024Jul 11, 2024

• Xenium_benchmarking

  Public
  Code used to benchmark Xenium

  Jupyter Notebook

  •6•39•4•0•Updated Jun 30, 2024Jun 30, 2024

• GBmap_ISS

  Public
  Code used in the publication "Harmonized single-cell landscape, intercellular crosstalk and tumor architecture of glioblastoma" for the analysis of ISS data

  Jupyter Notebook

  •0•0•0•0•Updated Apr 22, 2024Apr 22, 2024

• PLP_directRNA_design

  Public
  Package used to create padlock probes that target RNA directly. It can be used for any gene and species.

  Python

  •

  MIT License

  •1•0•1•0•Updated Jan 31, 2024Jan 31, 2024

• cellular-architecture-of-evolving-neuroinflammatory-lesions-and-multiple-sclerosis-pathology

  Public
  Jupyter Notebook

  •0•2•0•0•Updated Jan 29, 2024Jan 29, 2024

• ISS_postprocessing

  Public
  Jupyter Notebook

  •

  MIT License

  •0•1•0•0•Updated Sep 25, 2023Sep 25, 2023

• ISS_decoding

  Public
  Jupyter Notebook

  •0•1•1•1•Updated Sep 25, 2023Sep 25, 2023

• ISS_CARE

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Sep 25, 2023Sep 25, 2023

• ISS_deconvolution

  Public
  Repository to do image deconvolution on ISS datasets using Flowdec

  Jupyter Notebook

  •0•0•1•0•Updated Sep 25, 2023Sep 25, 2023

• ISS_preprocessing

  Public
  Python

  •1•2•3•0•Updated Sep 22, 2023Sep 22, 2023

• Sepsis

  Public
  Perl

  •0•0•0•0•Updated Jul 14, 2023Jul 14, 2023

• HDCA_Lung_reproducibility

  Public
  Repository containing all the code used for the manuscript Sountoulidis, Marco Salas et al.

  Jupyter Notebook

  •0•0•0•0•Updated Oct 4, 2022Oct 4, 2022

• DMG_HybISS

  Public
  Python (Jupyter Notebooks) and Matlab code used in Liu et al. 2022, Nature Genetics.

  Jupyter Notebook

  •0•0•0•0•Updated Sep 8, 2022Sep 8, 2022

• Tuberculosis-bacterial-analysis

  Public
  Repository including scripts related to the single bacteria identification and bacterial cluster identification for tuberculosis

  MATLAB

  •0•1•0•0•Updated Apr 29, 2022Apr 29, 2022

• HybrISS

  Public
  This repository includes the scripts and files assiciated with Hower ISS project

  MATLAB

  •0•1•1•0•Updated Apr 5, 2022Apr 5, 2022

• Matisse

  Public
  HTML

  •0•2•2•0•Updated Aug 2, 2021Aug 2, 2021

• pciseq_processing_module

  Public
  Python

  •0•0•0•0•Updated Oct 22, 2020Oct 22, 2020

• Tools

  Public
  Repository containing all the preprocessing and analysis tools generated in Molecular Diagnosis group, Science for Life Laboratories, Stockholm University, Sweden

  MATLAB

  •3•4•3•0•Updated Mar 7, 2020Mar 7, 2020

• data

  Public
  this repository contains data from the nilsson lab. it includes spot-by-gene matrices, cell-by-gene matrices , dapi images and the spatial locations of the cell centroids.

  0•0•0•0•Updated Feb 17, 2020Feb 17, 2020

• in_situ_seq

  Public
  Basic analysis pipeline for in situ sequencing

  MATLAB

  •

  GNU General Public License v3.0

  •2•5•0•0•Updated Jan 15, 2020Jan 15, 2020

• iss_starfish

  Public
  scripts used to format ISS data into StarFISH format

  HTML

  •

  MIT License

  •1•1•0•0•Updated Oct 7, 2019Oct 7, 2019

• iss-analysis

  Public
  Dump all scripts used to analyze iss data

  MATLAB

  •0•1•0•0•Updated Oct 4, 2019Oct 4, 2019

• ISSheart3D

  Public
  R

  •1•1•0•0•Updated Jul 12, 2019Jul 12, 2019

• heart

  Public
  scripts and viewer used for "A spatiotemporal organ-wide gene expression and cell atlas of the developing human heart"

  JavaScript

  •0•2•0•0•Updated Jul 12, 2019Jul 12, 2019

• ca1_atlas

  Public
  Misc. code used in "A spatial atlas of inhibitory cell types in mouse hippocampus"

  MATLAB

  •0•1•0•0•Updated Jun 4, 2019Jun 4, 2019

• tumor_heterogeneity

  Public
  scripts used in "Spatially resolved gene expression profiling identifies intratumoral diagnostic and prognostic heterogeneity in breast cancer."

  MATLAB

  •1•1•0•0•Updated May 13, 2019May 13, 2019

• tb_granuloma

  Public
  scripts used in "Spatial and temporal localization of immune transcripts defines hallmarks and diversityin the tuberculosis granuloma"

  MATLAB

  •0•0•0•0•Updated May 13, 2019May 13, 2019

• MolDia

  Public
  R package to analyze single cell in-situ sequencing (ISS) data

  R

  •1•1•0•0•Updated Dec 16, 2018Dec 16, 2018

• xy_dimorphism

  Public
  Code used in "Spatial sexual dimorphism of X and Y homolog gene expression in the human central nervous system during early male development"

  MATLAB

  •0•0•0•0•Updated Oct 24, 2018Oct 24, 2018