PedroMilanezAlmeida's starred repositories

scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

Language:PythonLicense:BSD-3-ClauseStargazers:1167Issues:28Issues:1003

Rcpp

Seamless R and C++ Integration

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fgsea

Fast Gene Set Enrichment Analysis

Language:RLicense:NOASSERTIONStargazers:354Issues:19Issues:125

PCAtools

PCAtools: everything Principal Components Analysis

miloR

R package implementation of Milo for testing for differential abundance in KNN graphs

Language:RLicense:GPL-3.0Stargazers:325Issues:9Issues:241

uwot

An R package implementing the UMAP dimensionality reduction method.

Language:RLicense:GPL-3.0Stargazers:313Issues:21Issues:108

scattermore

very fast scatterplots for R

Language:RLicense:GPL-3.0Stargazers:231Issues:8Issues:13

sctransform

R package for modeling single cell UMI expression data using regularized negative binomial regression

Language:RLicense:GPL-3.0Stargazers:203Issues:17Issues:180

ggdark

Dark mode for ggplot2 themes

Language:RLicense:NOASSERTIONStargazers:194Issues:10Issues:9

glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably

Language:RLicense:LGPL-3.0Stargazers:92Issues:9Issues:34

CelliD

Gene signature extraction and cell-identity recognition at individual cell level from single-cell RNA-seq.

Language:RLicense:GPL-3.0Stargazers:77Issues:6Issues:21

lemur

Latent Embedding Multivariate Regression

Language:RLicense:NOASSERTIONStargazers:75Issues:5Issues:15

Sanity

Filtering of Poison noise on a single-cell RNA-seq UMI count matrix

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dsb

Normalize CITEseq Data

Language:RLicense:NOASSERTIONStargazers:63Issues:10Issues:43

SCPA

R package for pathway analysis in scRNA-seq data

Language:RLicense:GPL-3.0Stargazers:56Issues:2Issues:59

miloDE

Framework for sensitive DE testing (using neighbourhoods)

Language:RLicense:NOASSERTIONStargazers:53Issues:3Issues:22

contrastive-ne

Contrastive neighbor embeddings

Language:Jupyter NotebookLicense:MITStargazers:51Issues:7Issues:4

scar

scAR (single-cell Ambient Remover) is a deep learning model for removal of the ambient signals in droplet-based single cell omics

umi-normalization

Companion repository to Lause, Berens & Kobak (2021): "Analytic Pearson residuals for normalization of single-cell RNA-seq UMI data", Genome Biology

Language:Jupyter NotebookLicense:AGPL-3.0Stargazers:40Issues:8Issues:3

rcpphnsw

Rcpp bindings for the approximate nearest neighbors library hnswlib

Language:C++License:GPL-3.0Stargazers:35Issues:6Issues:14

EmbedSOM

Fast embedding ot multidimensional datasets, great for cytometry data

Language:RLicense:GPL-3.0Stargazers:24Issues:5Issues:0

mrvi_archive

Multi-resolution Variational Inference

Language:PythonLicense:BSD-3-ClauseStargazers:22Issues:4Issues:4

scPrisma

scPrisma is a spectral analysis method, for pseudotime reconstruction, informative genes inference, filtering, and enhancement of underlying cyclic signals

Language:Jupyter NotebookLicense:MITStargazers:17Issues:2Issues:1
Language:RLicense:NOASSERTIONStargazers:15Issues:3Issues:7

rnndescent

R package implementing the Nearest Neighbor Descent method for approximate nearest neighbors

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Language:Jupyter NotebookLicense:BSD-3-ClauseStargazers:7Issues:8Issues:0
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