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

Intro to spatial analysis in R

Simulating single-cell data using gene regulatory networks 📠

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

A comprehensive tool for processing, analyzing and visulizing single cell chromatin accessibility sequencing data

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

A pure Nim k-d tree implementation for efficient spatial querying of point data

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

Kuwala is the no-code data platform for BI analysts and engineers enabling you to build powerful analytics workflows. We are set out to bring state-of-the-art data engineering tools you love, such as Airbyte, dbt, or Great Expectations together in one intuitive interface built with React Flow. In addition we provide third-party data into data sc…

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

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

A tool that allows to get UMI counts from a single cell protein assay

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

Methods for detecting doublets in single-cell sequencing data

Data and code related to the paper "ADAGE-Based Integration of Publicly Available Pseudomonas aeruginosa..." Jie Tan, et al · mSystems · 2016

Bead-based single-cell atac processing

Interactive R package to quantify, analyse and visualise alternative splicing

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

Proof of concept developer code and samples to help be successful with all ArcGIS developer products (Python, NET, JavaScript, Android…). The repository is designed to be an exchange for sharing coding conventions and wisdom to developers at all skill levels.

CUT&RUN and CUT&Tag data processing and analysis

R Package for accessing and plotting Google Maps

Tools for working with GTFS public transit data in ArcGIS

A curated set of lightweight but powerful tools for on-the-fly image processing and raster analysis in ArcGIS.

Tools for single-cell data processing

Long list of geospatial tools and resources

GREIN : GEO RNA-seq Experiments Interactive Navigator

Development version of 'spatstat' package ..............................

Spatial alignment of single cell transcriptomic data.

Powerful, efficient particle trajectory analysis in scientific Python.

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

GPstuff - Gaussian process models for Bayesian analysis

A spatial aware implementation of elliptical Fourier analysis

The zoon R package

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

Open framework for calculating spatial urban sprawl indices and performing disaggregated population estimates using open data

Convert between AnnData and SingleCellExperiment

R package for Bayesian spatial and spatiotemporal GLMMs with possible extremes

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

A cluster computing framework for processing large-scale geospatial data

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.

Repository contains pgRouting library. Development branch is "develop", stable branch is "master"

🌎 An R package for spatial and spatiotemporal GLMMs with TMB

The GIS Tools for Hadoop are a collection of GIS tools for spatial analysis of big data.

Single cell analysis in the browser

A Temporal Extension Library for PyTorch Geometric

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

Google Earth Engine for R

A tool for the spatial analysis of diversity

OSMnx: Python for street networks. Retrieve, model, analyze, and visualize street networks and other spatial data from OpenStreetMap.

Transcripts annotation and GO enrichment Fisher tests

Accumulated shadow data computed for New York City

Spatial Optimization

A Data Clinic project that aggregates NYC Open Data at the tract-level and uses Machine Learning techniques to re-imagine neighborhood boundaries.

📊 Gene expression in neuroexpresso database

Single-cell copy number calling and event history reconstruction.

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

🌎 Python library to access all public routing, isochrones and matrix APIs in a consistent manner.

Package with spatial analysis and spatial prediction tools

Multiome GRN inference.

Progression path for a GIS analyst who wants to become proficient in using Python for GIS: from apprentice to guru

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline