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Powsimr ⭐ 102

Power analysis is essential to optimize the design of RNA-seq experiments and to assess and compare the power to detect differentially expressed genes. PowsimR is a flexible tool to simulate and evaluate differential expression from bulk and especially single-cell RNA-seq data making it suitable for a priori and posterior power analyses.

R package that automatically classifies the cells in the scRNA data by segregating non-malignant cells of tumor microenviroment from the malignant cells. It also infers the copy number profile of malignant cells, identifies subclonal structures and analyses the specific and shared alterations of each subpopulation.

Multinichenetr ⭐ 56

MultiNicheNet: a flexible framework for differential cell-cell communication analysis from multi-sample multi-condition single-cell transcriptomics data

Identifying tumor cells at the single-cell level using machine learning

VoxHunt: Resolving human brain organoid heterogeneity through single-cell genomic comparison to spatial brain maps

Python tool for alignment of spatial transcriptomics (ST) data using diffeomorphic metric mapping

Imcdataanalysis ⭐ 22

R based workflow for multiplexed imaging data

A fast and accurate deconvolution algorithm based on regularized matrix completion algorithm (ENIGMA)

Scgeatoolbox ⭐ 21

scGEAToolbox: Matlab toolbox for single-cell gene expression analyses

Rpanglaodb ⭐ 17

An R package to download and merge labeled single-cell RNA-seq data from the PanglaoDB database into a Seurat object.

Omicssuite.github.io ⭐ 15

OmicsSuite website for releasing new version.

NASQAR: A web-based platform for High-throughput sequencing data analysis and visualization

Molecular interactions inference from single-cell multi-omics data

Scatac Mouse Human Control ⭐ 8

Mouse / human control of cross-contaminations in single-cell ATAC-seq on Fluidigm C1

A highly scalable and accurate inference of gene expression and structure for single-cell transcriptomes using semi-supervised deep learning.

Pixelator ⭐ 6

A command-line tool and library to process and analyze sequencing data from Molecular Pixelation (MPX) assays.

Yet another single-cell analysis toolkit

Hgg Oncohistones ⭐ 5

Analysis for "K27M in canonical and noncanonical H3 variants occurs in distinct oligodendroglial cell lineages in brain midline gliomas" (Jessa et al, Nature Genetics, 2022)

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