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R package to detect breakpoints and assign somies to scATAC-seq data
PHATE (Potential of Heat-diffusion for Affinity-based Transition Embedding) is a tool for visualizing high dimensional data.
Geometry Regularized Autoencoders (GRAE) for large-scale visualization and manifold learning
Supplementary code to reproduce key analyses and figures in the manuscript "Ultra-high scale cytometry-based cellular interaction mapping".
Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data
Foal-specific cell-Free DNA sequencing for Bacterial Identification
A collection of singularity definition files
Rcpp Machine Learning: Fast robust NMF, divisive clustering, and more
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene reg…
A proof of concept daisy-chaining Nextflow workflows
a generalist algorithm for cellular segmentation with human-in-the-loop capabilities
distfit is a python library for probability density fitting.
add statistical significance annotations on seaborn plots. Further development of statannot, with bugfixes, new features, and a different API.
A robust, extensible metagenomics pipeline
GenMap - Fast and Exact Computation of Genome Mappability
Locating genetic regions that are "just right"
FundaScaper scrapes data from Funda, the Dutch housing website. You can find listings from house-buying or rental market, and historical data. 🏡
A Practical and Efficient NCBI Taxonomy Toolkit, also supports creating NCBI-style taxdump files for custom taxonomies like GTDB/ICTV
Scalable creating/updating of metagenome profiling databases
BAM Statistics, Feature Counting and Annotation
accurate LiftOver tool for new genome assemblies
Modular command-line solution for visualisation, quality control and taxonomic partitioning of genome datasets
Ultra-fast and memory-efficient (meta-)genome assembler