gear-genomics / dicey Star 55 Code Issues Pull requests In-silico PCR, primer design and padlock design for in-situ sequencing primer padlock pcr amplicon primer-design amplicon-sequencing gear-genomics in-silico sanger-sequencing in-situ-sequencing Updated Aug 19, 2026 C++
wanglab-broad / ClusterMap Star 46 Code Issues Pull requests ClusterMap for multi-scale clustering analysis of spatial gene expression bioinformatics transcriptomics cell-segmentation single-cell-analysis spatial-transcriptomics in-situ-sequencing spatial-omics Updated Jun 13, 2025 Jupyter Notebook
wahlby-lab / spage2vec Star 13 Code Issues Pull requests spatial-data-analysis graphsage in-situ-hybridization in-situ-sequencing Updated Jul 1, 2021 Jupyter Notebook
broadinstitute / pooled-cell-painting-profiling-recipe Star 7 Code Issues Pull requests Recipe for profile creation for pooled image-based/morphological profiling (including Cell Painting) experiments data-science recipe pooled-screen cell-painting morphological-profiling pooled-cell-painting in-situ-sequencing Updated Aug 5, 2026 Python
LiuLab-Bioelectronics-Harvard / ClusterMap Star 6 Code Issues Pull requests ClusterMap for multi-scale clustering analysis of spatial gene expression bioinformatics transcriptomics cell-segmentation single-cell-analysis spatial-transcriptomics in-situ-sequencing spatial-omics Updated Feb 14, 2022 Jupyter Notebook
broadinstitute / pooled-cell-painting-profiling-template Star 2 Code Issues Pull requests 🛠️ Use me to version control Pooled Cell Painting data and processing pipelines pooled-screen cell-painting carpenter-lab pooled-cell-painting template-repository in-situ-sequencing Updated May 21, 2024 Python
gear-genomics / padlock Star 1 Code Issues Pull requests Design padlock probes for in-situ sequencing genomics probes probe-design in-situ-sequencing Updated Apr 7, 2026 HTML