139 Open source projects that are alternatives of or similar to MERINGUE

Inference of switch-like differential expression along single-cell trajectories

R package to do the Ligand Receptor Analysis Visualization

Spatial Single Cell Analysis in Python

spatial transcriptome, single cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

Fast visualization tool for large-scale and high dimensional single-cell data

Differential Gene Correlation Analysis

Covarying neighborhood analysis (CNA) is a method for finding structure in- and conducting association analysis with multi-sample single-cell datasets.

TCGA data acquisition and processing for Project Cognoma

Efficient genotyping bi-allelic SNPs on single cells

Cell type specific enrichments using finemapped variants and quantitative epigenetic data

GCModeller: genomics CAD(Computer Assistant Design) Modeller system in .NET language

Learning cell communication from spatial graphs of cells

No description or website provided.

Automatic Annotation on Cell Types of Clusters from Single-Cell RNA Sequencing Data

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

R API and htmlwidget for Vitessce

Single-Cell Omics Preparation Entity Tools

sabre: Spatial Association Between REgionalizations

A Geometry library for Elixir that calculates spatial relationships between two geometries

mgatk: mitochondrial genome analysis toolkit

bring sf to spark in production

A tool for semi-automatic cell type annotation

R package to access DoRothEA's regulons

Mouse cell atlas

Enjoy your transcriptomic data and analysis responsibly - like sipping a cocktail

Spatial Modelling for Data Scientists

Remote Sensing and GIS Software Library; python module tools for processing spatial data.

Intro to spatial analysis in R

R package: Simulate Expression data from igraph network using mvtnorm (CRAN; JOSS)

Data analysis scripts for Datlinger et. al, 2017 (doi:10.1038/nmeth.4177)

R package (compatible with SCope) to create generic .loom files and extend them with other data e.g.: SCENIC regulons, Seurat clusters and markers, ...

Non-official Git repository for R package cellrangerRkit (currently not available elsewhere; I'm not affiliated with 10x)

Graph-linked unified embedding for single-cell multi-omics data integration

Methods for detecting doublets in single-cell sequencing data

Bead-based single-cell atac processing

🧬 Immunarch by ImmunoMind: R Package for Fast and Painless Exploration of Single-cell and Bulk T-cell/Antibody Immune Repertoires

CUT&RUN and CUT&Tag data processing and analysis

Tools for working with GTFS public transit data in ArcGIS

Tools for single-cell data processing

GREIN : GEO RNA-seq Experiments Interactive Navigator

Spatial alignment of single cell transcriptomic data.

Differential expression (DE); gene set Enrichment Analysis (GSEA); single cell RNAseq studies (scRNAseq)

A spatial aware implementation of elliptical Fourier analysis

A COBRApy extension for genome-scale models of metabolism and expression (ME-models)

Convert between AnnData and SingleCellExperiment

An introductory course on using R for geographic data visualisation and analysis (in Russian).

A Python implementation of the model described in our publication "A convolutional neural network for common-coordinate registration of high-resolution histology images" developed principally for applications to registration of spatial transcriptomics image data.

🌎 An R package for spatial and spatiotemporal GLMMs with TMB

Single cell analysis in the browser

An online companion to the OSCA manuscript demonstrating Bioconductor resources and workflows for single-cell RNA-seq analysis.

A tool for the spatial analysis of diversity

Transcripts annotation and GO enrichment Fisher tests

R package to visualize gene expression data based on weighted kernel density estimation

Spatial Optimization

📊 Gene expression in neuroexpresso database

kallisto | bustools workflow for pre-processing single-cell RNA-seq data

Conditional out-of-distribution prediction

This repository contains the tensorflow implementation of "GNE: A deep learning framework for gene network inference by aggregating biological information"

PECA is a software for inferring context specific gene regulatory network from paired gene expression and chromatin accessibility data