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acme

This repository contains open-source C++ code for reconstructing membranes from time-lapse confocal/2-photon image data. Please refer to the webpage below for detailed instructions, precompiled binaries, and sample data for testing the code.

celda

Bayesian Hierarchical Modeling for Clustering Single Cell RNA-Seq Data

cellpose

a generalist algorithm for cellular segmentation with human-in-the-loop capabilities

cho_xi_seqscope

Seqscope codes

counterfactual_dim_reduction_sc

A novel dimension reduction based on Structural Causal Model (SCM)

dropest

Pipeline for initial analysis of droplet-based single-cell RNA-seq data

imageclipr

RStudio Addin: Copy Image from Clipboard into RMarkdown .Rmd file

indrops

Pipeline for processing inDrops sequencing data

insitu_probe_generator

Generate HCR-style Probe Pairs for mRNA visualization

lpc-reprogramming

magic

MAGIC (Markov Affinity-based Graph Imputation of Cells), is a method for imputing missing values restoring structure of large biological datasets.

mtsa-tutorial

presto

Fast Wilcoxon and auROC

rdpca

Read-depth aware principal component analysis

seurat

R toolkit for single cell genomics

singler

SingleR: Single-cell RNA-seq cell types Recognition

tn_test

post-clustering differential expression test

trackhub

trackhub2