Reverse Dependencies of loompy

The following projects have a declared dependency on loompy:

• anndata — Annotated data.
• astir — no summary
• BlueWhale3-SingleCell — Add-on for bioinformatics analysis of single cell data.
• candig-rnaget — A POC implementation of GA4GH RNAGET API
• Cell-BLAST — Single-cell transcriptome querying tool
• cellbender — A software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data
• cellex — Compute single-cell cell-type expression specificity
• descartes-rpa — descartes_rpa: Extract pathway features from Single-Cell
• dynamo-release — Mapping Vector Field of Single Cells
• fgread — Module for reading datasets shared on FASTGenomics
• ga4gh-rnaget-compliance — Reports web service compliance to GA4GH RNAget specification
• loomxpy — Python package to create .loom files (compatible with SCope) and extend them with other data (e.g.: SCENIC regulons)
• matrix-semantic-map — Semantic mapper for Loom file metadata.
• monod — the Monod package fits CME models to sequencing data.
• mrvi — Multi-resolution analysis of single-cell data.
• multivelo — Multi-omic extension of single-cell RNA velocity
• neuralee — NeuralEE: a GPU-accelerated elastic embedding dimensionality reduction method for visualization of large-scale scRNA-seq data
• ngs-toolkit — A toolkit for NGS analysis with Python.
• Orange3-SingleCell — Add-on for bioinformatics analysis of single cell data.
• pegasusio — Pegasusio is a Python package for reading / writing single-cell genomics data
• pegasuspy — Pegasus is a Python package for analyzing sc/snRNA-seq data of millions of cells
• pyBCS-bioturing — Create BioTuring Compressed Study (bcs) file
• SC-search — Single-cell search tool
• scanpy-scripts — Scripts for using scanpy from the command line
• scCloud — scRNA-Seq analysis tools that scale to millions of cells
• scgen — ScGen - Predicting single cell perturbations.
• scp-ingest-pipeline — ETL pipeline for single-cell RNA-seq data
• sctreeshap — sctreeshap: a cluster tree data structure, and for shap analysis
• scvae — Model single-cell transcript counts using deep learning.
• scvelo — RNA velocity generalized through dynamical modeling
• scvi — Single-cell Variational Inference
• scvi-tools — Deep probabilistic analysis of single-cell omics data.
• scvr — single cell VR preprocess
• scvr-prep — single cell VR preprocess
• sfaira — sfaira is a model and a data repository for single-cell data in a single python package.
• sopa — Spatial-omics pipeline and analysis
• spateo-release — Spateo: multidimensional spatiotemporal modeling of single-cell spatial transcriptomics
• topicvelo — TopicVelo: Dissection and Integration of Bursty Transcriptional Dynamics for Complex Systems
• velodyn — Dynamical systems approaches for RNA velocity analysis
• vitessce — Jupyter widget facilitating interactive visualization of spatial single-cell data with Vitessce