bhavyaac

poetry

Python packaging and dependency management made easy

FriendsDontLetFriends

Friends don't let friends make certain types of data visualization - What are they and why are they bad.

scGPT

single-cell-pseudotime

An overview of algorithms for estimating pseudotime in single-cell RNA-seq data

CellBender

CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

SoupX

R package to quantify and remove cell free mRNAs from droplet based scRNA-seq data

grateful

Facilitate citation of R packages

scenicplus

SCENIC+ is a python package to build gene regulatory networks (GRNs) using combined or separate single-cell gene expression (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) data.

single-cell-transformer-papers

dictys

Context specific and dynamic gene regulatory network reconstruction and analysis

awesome-foundation-model-single-cell-papers

voyager

From geospatial to spatial -omics

semla

loom-viewer

Tool for sharing, browsing and visualizing single-cell data stored in the Loom file format

scLearn

scLearn：Learning for single cell assignment

MERlin

MERFISH decoding software

ClusterDE

A post-clustering differential expression (DE) method robust to false-positive inflation caused by double dipping

sync-paperpile-notion

Sync changes in Paperpile to a Notion database.

DSPIN

Code and example of the D-SPIN framework

yascp

scRNA multimodal analysis pipeline utilised for large dataset processing

CRAWDAD

Cell-type Relationship Analysis Workflow Done Across Distances

fetal_brain_multiomics

Supplementary files and notebooks to recreate figures.

MoleculeExperiment

chromograph

Camiel's scATAC-seq analysis pipeline

scReClassify

Post hoc cell type classification of single-cell RNA-sequencing data.

BGP_2023

CalicoST

Inferring allele-specific copy number aberrations and tumor phylogeography from spatially resolved transcriptomics

hooke

A package for comparing cell type abundances between conditions

liam

DeepTools