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awesome_spatial_omics

tools and notes for spatial omics

bambu

Reference-guided transcript discovery and quantification for long read RNA-Seq data

banksy-bioc2024

banksy-zenodo

Scripts to reproduce BANKSY analyses.

bayesspace

Bayesian model for clustering and enhancing the resolution of spatial gene expression experiments.

daiso

Degradation-aware isoform quantification

escnn

Equivariant Steerable CNNs Library for Pytorch

fict-sample

Depository for the sample code using FICT

hello-world

icp

A Python implementation of the Iterative Closest Point algorithm

latex-templates

Commented templates for CVs, homework, lecture notes, presentations, research papers, and essays, with commands for math/statistics symbols

mahotas

Computer Vision in Python

muse

MUSE is a deep learning approach characterizing tissue composition through combined analysis of morphologies and transcriptional states for spatially resolved transcriptomics data.

neural-processes

PyTorch implementation of latent neural processes.

pcurvepy

Principal curves implementation (Hastie '89) in Python

proactiv

Estimation of Promoter Activity from RNA-Seq data

pytorch-model-compare

Compare neural networks by their feature similarity

qeval

rcav2

R package for robust clustering of single cell RNA sequencing data

rigraph

igraph R package

schelpers

Helper functions for single cell analyses

seurat-wrappers

Community-provided extensions to Seurat

stellargraph

StellarGraph - Machine Learning on Graphs

trackviewer

A bioconductor package with minimalist design for drawing elegant tracks or lollipop plot

zb4171-project

zb4199-thesis