Molecular Diagnostics (Mats Nilsson research group)

multi_padlock_design

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

Tools

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

in_situ_seq

Basic analysis pipeline for in situ sequencing

heart

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

ISS_preprocessing

ca1_atlas

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

HybrISS

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

iss-analysis

Dump all scripts used to analyze iss data

ISS_decoding

ISS_postprocessing

iss_starfish

scripts used to format ISS data into StarFISH format

ISSheart3D

Matisse

MolDia

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

Tuberculosis-bacterial-analysis

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

tumor_heterogeneity

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

data

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.

DMG_HybISS

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

HDCA_Lung_reproducibility

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

ISS_CARE

ISS_deconvolution

Repository to do image deconvolution on ISS datasets using Flowdec

pciseq_processing_module

PLP_directRNA_design

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

Sepsis

tb_granuloma

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

xy_dimorphism

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