PedroMilanezAlmeida's starred repositories

miloDE

Framework for sensitive DE testing (using neighbourhoods)

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EmbedSOM

Fast embedding ot multidimensional datasets, great for cytometry data

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

lemur

Latent Embedding Multivariate Regression

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mrvi_archive

Multi-resolution Variational Inference

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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:0Issues:0

CelliD

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

Language:RLicense:GPL-3.0Stargazers:76Issues:0Issues:0

glmGamPoi

Fit Gamma-Poisson Generalized Linear Models Reliably

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SCPA

R package for pathway analysis in scRNA-seq data

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uwot

An R package implementing the UMAP dimensionality reduction method.

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sctransform

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

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miloR

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

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scar

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

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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:0Issues:0

contrastive-ne

Contrastive neighbor embeddings

Language:Jupyter NotebookLicense:MITStargazers:50Issues:0Issues:0

fgsea

Fast Gene Set Enrichment Analysis

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ggdark

Dark mode for ggplot2 themes

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scattermore

very fast scatterplots for R

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scvi-tools

Deep probabilistic analysis of single-cell and spatial omics data

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Sanity

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

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dsb

Normalize CITEseq Data

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rnndescent

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

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Rcpp

Seamless R and C++ Integration

Language:C++License:GPL-2.0Stargazers:723Issues:0Issues:0

rcpphnsw

Rcpp bindings for the approximate nearest neighbors library hnswlib

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PCAtools

PCAtools: everything Principal Components Analysis

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