Alexandru-Emil

Alexandru-Emil's Stars

• NBISweden/workshop-epigenomics-RTDs

  workshop website on readthedocs

  1613

• mildpiggy/DEP2

  An r package for proteomics data Analysis, developed from DEP.

  Language:R142

• gustaveroussy/sopa

  Technology-invariant pipeline for spatial omics analysis (Xenium / MERSCOPE / CosMx / PhenoCycler / MACSima / Hyperion) that scales to millions of cells

  Language:Python10610

• saezlab/DOT

  DOT

  Language:R7

• nolanlab/vortex

  VorteX Clustering Environment - Java graphical tool for single-cell analysis, clustering and visualization. Latest release:

  Language:Java346

• nolanlab/TissueSchematics

  Code accompanying the manuscript "Tissue Schematics map the specialization of immune tissue motifs and their appropriation by tumors"

  Language:Jupyter Notebook102

• snap-stanford/stellar

  Language:Jupyter Notebook5817

• SGDDNB/translational_regulation

  Detection of differential translated genes using Ribo-seq

  Language:R1311

• CarvunisLab/iRibo

  iRibo

  Language:C++2

• nf-core/riboseq

  Pipeline for the analysis of ribosome profiling, or Ribo-seq (also named ribosome footprinting) data.

  Language:Nextflow54

• ftwkoopmans/msdap

  MS-DAP: downstream analysis pipeline for quantitative proteomics

  Language:R286

• nf-core/quantms

  Quantitative mass spectrometry workflow. Currently supports proteomics experiments with complex experimental designs for DDA-LFQ, DDA-Isobaric and DIA-LFQ quantification.

  Language:Nextflow30

• yuqiuzhou/Pianno

  2

• quon-titative-biology/scProjection

  Projecting RNA measurements onto single cell atlases to extract cell type-specific expression profiles using scProjection

  Language:Python132

• YangLabHKUST/SpatialScope

  A unified approach for integrating spatial and single-cell transcriptomics data by leveraging deep generative models

  Language:Python495

• tgirke/systemPipeR

  Project Website:

  Language:R5238

• ColemanRHarris/mxnorm

  R package to normalize multiplexed imaging data.

  Language:R52

• systemPipeR/SPatacseq

  Workflow Template

  Language:TeX1

• dmcable/spacexr

  Spatial-eXpression-R: Cell type identification (including cell type mixtures) and cell type-specific differential expression for spatial transcriptomics

  Language:HTML28771

• aicplane/Linkage

  An R shiny web server for linking of ATAC-seq to gene expression data

  Language:R21

• satijalab/azimuth

  A Shiny web app for mapping datasets using Seurat v4

  Language:HTML10328

• C3BI-pasteur-fr/UTechSCB-SCHNAPPs

  Shiny app for the analysis of single cell data

  Language:R242

• interactivereport/scRNAsequest

  scRNASequest: an ecosystem of scRNA-seq analysis, visualization and publishing

  Language:R20

• seandavi/awesome-single-cell

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

  3.1k960

• YosefLab/VISION

  Signature Analysis and Visualization for Single-Cell RNA-seq

  Language:R15231

• mdozmorov/scRNA-seq_notes

  A list of scRNA-seq analysis tools

  Language:R607144

• ncats/public_sequin

  public production version of sequin to share with the public

  Language:HTML103

• morris-lab/CellOracle

  This is the alpha version of the CellOracle package

  Language:Python29751

• theislab/scCODA

  A Bayesian model for compositional single-cell data analysis

  Language:Jupyter Notebook14623

• LewisLabUCSD/Celegans-cell2cell

  Analyses for cell-cell interactions in C. elegans

  Language:Jupyter Notebook61