This is the repository for the single-cell transcriptomics application of the Deep Generative Decoder (DGD), developed by the Krogh group.

InstaPrism is an R package for fast implementation of BayesPrism

xCell 2.0: Robust Cell Type Enrichment Analysis

Monte Carlo tree search in JAX

f.k.a. Awesome ChatGPT Prompts. Share, discover, and collect prompts from the community. Free and open source — self-host for your organization with complete privacy.

Deep learning-based tissue compositions and cell-type-specific gene expression analysis with tissue-adaptive autoencoder (TAPE)

Statistical Rethinking course winter 2022

Here we describe an extension of MinHash that permits accurate compositional analysis of metagenomes with low memory and disk requirements.

Processing workflow for COVID-19 single cell data

Multiple trajectory alignment of time-series data

Single Cell Genomics for Enhancing Cell Composition Inference from Bulk Genomics Data

Feature Ranking in (possibly large) Clustered Single Cell Data

A bit-packed k-mer representation (and relevant utilities) for rust

Extensible, parallel implementations of t-SNE

Single-cell identity definition using random forest modelling and recursive feature elimination

Fast and memory-efficient clustering + coreset construction, including fast distance kernels for Bregman and f-divergences.

Iterative merging of clusters to improve mean ARI

Trajectory inference and differential expression over multiple conditions in scRNA-seq

Tool for decomposition centromeric assemblies and long reads into monomers

🔶 Compressed bitvector/container supporting efficient random access and rank queries

Hierarchical, iterative clustering for analysis of transcriptomics data in R

A docker image for single-cell analysis

another book on data science

A collection of 50+ trajectory inference methods within a common interface 📥📤

Formalizing and benchmarking open problems in single-cell genomics

base-accurate DNA sequence alignments using WFA and mashmap3

Content for the OSCA Book.