Pinned Repositories
anndata
Annotated data.
basic_flask_template
Simple flask server for display static image results
genevector
Vector representations of gene co-expression in single cell RNAseq.
grimoire
Magical spells for simple scRNA tasks.
gseapynet
Running GSEA with network view of pathways.
Hebbian
Boolean Hebbian learning framework
nceglia.github.io
Nick's blog
pycurve
scrna-pipeline
shah lab rnaseq pipeline
tcri
Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing
nceglia's Repositories
nceglia/genevector
Vector representations of gene co-expression in single cell RNAseq.
nceglia/tcri
Information Theoretic Framework for Paired Single Cell Gene Expression and TCR Sequencing
nceglia/scrna-pipeline
shah lab rnaseq pipeline
nceglia/gseapynet
Running GSEA with network view of pathways.
nceglia/nceglia.github.io
Nick's blog
nceglia/anndata
Annotated data.
nceglia/basic_flask_template
Simple flask server for display static image results
nceglia/grimoire
Magical spells for simple scRNA tasks.
nceglia/cellassign-1
Automated, probabilistic assignment of cell types in scRNA-seq data
nceglia/cellassign-tool
Container for running cellassign.
nceglia/clonealign
Bayesian inference of clone-specific gene expression estimates by integrating single-cell RNA-seq and single-cell DNA-seq data
nceglia/clonealign-tool
Container for running clonealign.
nceglia/CRI_bioinformatics_workshop
Tutorials and code for CRI bioinformatics workshop.
nceglia/fastmi
Rust binding for mutual information calculation.
nceglia/genevector-documentation
GeneVector Documentation and Tutorials
nceglia/HoneyBADGER
HMM-integrated Bayesian approach for detecting CNV and LOH events from single-cell RNA-seq data
nceglia/met_cohort_16428
Bladder cancer analysis
nceglia/mudata
Multimodal Data (.h5mu) implementation for Python
nceglia/muon
muon is a multimodal omics Python framework
nceglia/rnascp
Pure rust singe cell rnaseq pseudo alignment pipeline.
nceglia/RNASecondaryStructure
Genetic Algortihm
nceglia/rust-debruijn
De Bruijn graphs in Rust
nceglia/rust-pseudoaligner
Single-Cell RNA-seq pseudo-aligner
nceglia/scanpy
Single-cell analysis in Python. Scales to >1M cells.
nceglia/scirpy
A scanpy extension to analyse single-cell TCR and BCR data.
nceglia/scvis-tool
Container for scvis.
nceglia/spacevector
Spatial Vector Library
nceglia/spatialdata
An open and universal framework for processing spatial omics data
nceglia/squidpy
Spatial Single Cell Analysis in Python
nceglia/word2vec-pytorch
Extremely simple and fast word2vec implementation with Negative Sampling + Sub-sampling