Anna Rychkova's starred repositories
nn-zero-to-hero
Neural Networks: Zero to Hero
idemuxcpp
iDemux is an all-in-one command line tool that can be used for both demultiplexing and error correction of FASTQ files. It enables demultiplexing of i1 inline barcodes of Lexogen’s QuantSeq-Pool as well as demultiplexing of i7 and/or i5 indices of any other RNA-Seq library prep. iDemux can also be used for superior error correction of RNA-Seq libraries generated with Lexogen’s UDI 12 nt Unique Dual Indices. This C++ version is faster than the Python version but requires a certain proficiency in command line tool handling.
gatk4-rnaseq-germline-snps-indels
Workflows for processing RNA data for germline short variant discovery with GATK v4 and related tools
alzheimers_parkinsons
Collaboration with Montine, Chang, and Montgomery labs on Alzheimers / Parkinson's ATAC-seq analysis
metanetwork
metanetwork
awesome-bioinformatics-benchmarks
A curated list of bioinformatics bench-marking papers and resources.
omicsplayground
Visual self-service analytics platform for big omics data.
ShinyStudio
A fully Dockerized, self-hosted development environment for teams. Develop where you serve.
crowdcount-cascaded-mtl
Single Image Crowd Counting (CNN-based Cascaded Multi-task Learning of High-level Prior and Density Estimation for Crowd Counting)
single-cell-tutorial
Single cell current best practices tutorial case study for the paper:Luecken and Theis, "Current best practices in single-cell RNA-seq analysis: a tutorial"
public-resources
Repository for resources we'd like to share with the community.
gene_lists
List of gene lists for genomic analyses.
geneSynonym
Quick access to gene synonyms
regexplain
🔍 An RStudio addin slash regex utility belt
gwas_scripts
Codebook from my GWAS cookbook
genecircuits
Inference of tissue-specific transcriptional regulatory circuits