p-lombard

p-lombard's Stars

• SpatialTranscriptomicsResearch/st_pipeline

  ST Pipeline contains the tools and scripts needed to process and analyze the raw files generated with the Spatial Transcriptomics method in FASTQ format.

  Language:Python8030

• renozao/NMF

  NMF: A Flexible R package for Nonnegative Matrix Factorization

  Language:R13740

• asncd/schimera

  Language:Jupyter Notebook75

• willtownes/spatial-factorization-py

  Probabilistic factor models for spatially correlated data. Includes nonnegative and real-valued versions.

  Language:Python132

• dylkot/cNMF

  Code and example data for running Consensus Non-negative Matrix Factorization on single-cell RNA-Seq data

  Language:Jupyter Notebook27057

• seasoncloud/Clonalscope

  Clonalscope is a subclone detection method based on copy number alterations (CNAs) for single-cell and ST tumor sequencing data. Clonalscope is able to detect subclones, label malignant cells, and trace subclones for both scRNA-seq and ST data.

  Language:R12

• willtownes/nsf-paper

  Nonnegative spatial factorization for multivariate count data

  Language:Jupyter Notebook5511

• gevaertlab/GBM360

  Spatial cellular architecture predicts prognosis in glioblastoma - Nature Communications

  Language:Python182

• tiroshlab/3ca

  Code for reproducing the analysis in Gavish et al. "The transcriptional hallmarks of intra-tumor heterogeneity across a thousand tumors".

  Language:R729

• gabrielakinker/CCLE_heterogeneity

  Language:R5315

• scverse/scanpy

  Single-cell analysis in Python. Scales to >1M cells.

  Language:Python1.9k597

• tiroshlab/Spatial_Glioma

  Code for major analyses in "Integrative spatial analysis reveals a multi-layered organization of glioblastoma" paper

  Language:R336

• jpmam1/scalop

  Single Cell Analysis Operations

  Language:R56

• giovp/spatialdata-sandbox

  Language:Jupyter Notebook1014

• dpeerlab/SEACells

  SEACells algorithm for Inference of transcriptional and epigenomic cellular states from single-cell genomics data

  Language:Jupyter Notebook14527

• dpeerlab/scKINETICS

  Code for scKINETICS (ISMB 2023)

  Language:Jupyter Notebook203

• lucgar/GBMstates

  Scripts from the GBM cellular states paper

  1

• QuKunLab/SpatialBenchmarking

  Language:Jupyter Notebook10726

• azizilab/starfysh

  Spatial Transcriptomic Analysis using Reference-Free auxiliarY deep generative modeling and Shared Histology

  Language:Jupyter Notebook10113

• miccec/GBMstates

  Scripts from the GBM cellular states paper

  Language:HTML185

• jlaffy/hotmap

  Plot Pretty Easy Heatmaps In R

  Language:R2

• mbernste/SpatialCorr

  SpatialCorr: Identify gene sets with spatially varying correlation

  Language:Jupyter Notebook114

• lazappi/clustree

  Visualise Clusterings at Different Resolutions

  Language:R21415

• heilandd/SPATAwrappers

  Additional SPATA functions

  Language:R61

• tiroshlab/scrabble

  Perform Exploratory Computational Analyses on Processed Single-Cell RNA-Sequencing Data

  Language:R2

• theMILOlab/SPATA2

  A Toolbox for Spatial Transcriptomics Analysis

  Language:R9917

• ccruizm/GBmap

  Code used to create the core and extended GBmap, including downstream analyses (cell-cell interactions, spatial transcriptomics deconvolution) and how to produce the figures.

  Language:Jupyter Notebook4910

• romain-lopez/DestVI-reproducibility

  Reproducing the experiments of the DestVI paper

  Language:Jupyter Notebook176

• scverse/scvi-tutorials

  Notebooks used in scvi-tools tutorials

  Language:Jupyter Notebook4525

• rchanoch/MES_GBM_GENOME_MED

  "­­Elucidating the diversity of malignant mesenchymal states in glioblastoma by integrative analysis"

  5