103 Open source projects that are alternatives of or similar to Tangram

characterizing spatial gene expression heterogeneity in spatially resolved single-cell transcriptomics data with nonuniform cellular densities

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

📊 Gene expression in neuroexpresso database

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

GREIN : GEO RNA-seq Experiments Interactive Navigator

Transcripts annotation and GO enrichment Fisher tests

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

Haystack: Epigenetic Variability and Transcription Factor Motifs Analysis Pipeline

Differential Gene Correlation Analysis

TCGA data acquisition and processing for Project Cognoma

An unofficial demultiplexing strategy for SPLiT-seq RNA-Seq data

Examples using Clustergrammer2 to explore high-dimensional datasets.

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

Validation and manipulation of FASTQ files, scRNA-seq barcode pre-processing and UMI quantification.

Deep learning model for single-cell inference of multi-omic profiles from a single input modality.

Reference mapping for single-cell genomics

Papers with code for single cell related papers

Reconstruction of complex single-cell trajectories using CellRouter

Conversion between scRNA-seq objects

Harmony framework for connecting scRNA-seq data from discrete time points

Single-cell Hierarchical Poisson Factorization

cTPnet Package

A tool for semi-automatic cell type annotation

BEER: Batch EffEct Remover for single-cell data

Toolkit for highly memory efficient analysis of single-cell RNA-Seq, scATAC-Seq and CITE-Seq data. Analyze atlas scale datasets with millions of cells on laptop.

SHARP: Single-cell RNA-seq Hyper-fast and Accurate processing via ensemble Random Projection

Efficient and precise single-cell reference atlas mapping with Symphony

Demultiplexing pooled scRNA-seq data with or without genotype reference

Long list of geospatial tools and resources

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

R package with large datasets for spatial analysis

COVID-19 relevant data on hospital location / capacity, nursing home location / capacity, county demographics

S4SS: Statistics for Soil Survey

Spatial Containers, Pareto Fronts, and Pareto Archives

An elixir implementation of Rtree, optimized for fast updates.

R Interface for OGC Web-Services (OWS)

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

R Package: Regularized Principal Component Analysis for Spatial Data

R bindings for Google's s2 library for geometry on the sphere

DashMap is an open source web platform that gathers, analyses and visualises urban data.

A general form for complex data

An R package for quickly mapping and navigating spatial data

Spatial Transcriptomics human DLPFC pilot study part of the spatialLIBD project