chulaihunde

ann-benchmarks

Benchmarks of approximate nearest neighbor libraries in Python

awesome-single-cell

Community-curated list of software packages and data resources for single-cell, including RNA-seq, ATAC-seq, etc.

fbpca

Fast Randomized PCA/SVD

scRNA-tools

Table of software for the analysis of single-cell RNA-seq data.

Neighbor2Neighbor

Neighbor2Neighbor: Self-Supervised Denoising from Single Noisy Images

SAVER

Single-cell RNA-seq Gene Expression Recovery

metacell

Metacell - Single-cell mRNA Analysis

lpproj

Scikit-learn compatible Locality Preserving Projections in Python

knn-smoothing

K-nearest neighbor smoothing for high-throughput single-cell RNA-Seq data

mapr2

netNMF-sc

netNMF-sc: A network regularization algorithm for dimensionality reduction and imputation of single-cell expression data

tGPLVM

tGPLVM: A Nonparametric, Generative Model for Manifold Learning with scRNA-seq experimental data

SNN-Cliq

An algorithm used to classify the cell types from single cell rna sequence data.

scDGD

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

bmvae

a variational autoencoder method for clustering single-cell mutation data

autoCell

gplvm_scrna

Scalable GPLVMs for scRNA

TS-LPP

Two Step Locality Preserving Projections (TS-LPP)

dgd

latexOCRApi

A Latex OCR API based on [LaTex-OCR](https://github.com/lukas-blecher/LaTeX-OCR) and [fastApi](https://github.com/tiangolo/fastapi)

scRNAseq_AdipocyteSubtyping

Python pipelines for analysis of adipocyte scRNA-seq data

ZIPPCA

Zero-Inflated Probabilistic PCA (ZIPPCA), for dimension reduction and data ordination of multivariate abundance data, and propose an efficient variational approximation method for estimation, inference, and prediction.

coexpression_graph

Python modules for the calculation of coexpression graph and affinity matrix, based on expression profiles

abc4pwm

affinity based clustering for position weight matrix

PNN_LPP

Probabilistic Nearest Neighbor based Locality Preserving Projections

sawkde

Gaussian Kernel Density Estimation with Selective-Adaptive Bandwidth

netImpute

scRNAseq

A pipeline for chaining together single cell RNA seq tasks

NetID

The pipeline for benchmarking NetID with different imputation methods on any UMI-based scRNA-seq datasets

Denoising_THG

Self-Supervised Image Denoising of Third Harmonic Generation Microscopic Images of Human Glioma Tissue by Transformer-based Blind Spot (TBS) Network