kris96tian/sc-RNAseq_analysis

Single-cell RNA data analysis using R (Seurat) , Python (Scanpy), and Julia.

Language: Jupyter Notebook - Size: 4.53 MB - Last synced: about 8 hours ago - Pushed: about 9 hours ago - Stars: 0 - Forks: 0

scverse/scanpy

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

Language: Python - Size: 37.9 MB - Last synced: about 7 hours ago - Pushed: about 7 hours ago - Stars: 1,773 - Forks: 577

YosefLab/pycea

scverse lineage tracing analysis toolkit

Language: Python - Size: 291 KB - Last synced: about 11 hours ago - Pushed: about 24 hours ago - Stars: 0 - Forks: 0

theislab/anndata2ri

Convert between AnnData and SingleCellExperiment

Language: Python - Size: 178 KB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 114 - Forks: 16

viktormiok/scRNAseq_AdipocyteSubtyping

Python pipelines for analysis of adipocyte scRNA-seq data

Language: Jupyter Notebook - Size: 521 KB - Last synced: 3 days ago - Pushed: 3 days ago - Stars: 4 - Forks: 3

YosefLab/treedata

anndata with trees

Language: Python - Size: 291 KB - Last synced: 1 day ago - Pushed: 3 days ago - Stars: 1 - Forks: 1

kaderhoussein/sc_oop

Interactive diffusion map for Single-Cell Data Analysis

Language: Python - Size: 2.55 MB - Last synced: 4 days ago - Pushed: 4 days ago - Stars: 0 - Forks: 0

scverse/muon

muon is a multimodal omics Python framework

Language: Python - Size: 5.04 MB - Last synced: 5 days ago - Pushed: 16 days ago - Stars: 197 - Forks: 28

lilab-bcb/cirrocumulus

Bring your single-cell data to life

Language: JavaScript - Size: 223 MB - Last synced: 4 days ago - Pushed: 17 days ago - Stars: 64 - Forks: 10

scverse/anndata

Annotated data.

Language: Python - Size: 4.33 MB - Last synced: 24 days ago - Pushed: 24 days ago - Stars: 501 - Forks: 150

stefanpeidli/mousipy

Translates an AnnData object with mouse gene symbols into one with human gene symbols by mapping orthologs from biomart.

Language: Jupyter Notebook - Size: 14.9 MB - Last synced: 13 days ago - Pushed: 2 months ago - Stars: 14 - Forks: 3

theislab/ncem

Learning cell communication from spatial graphs of cells

Language: Python - Size: 40.8 MB - Last synced: 18 days ago - Pushed: 4 months ago - Stars: 96 - Forks: 13

becavin-lab/checkatlas

One liner tool to check the quality of your single-cell atlases.

Language: HTML - Size: 51.9 MB - Last synced: 27 days ago - Pushed: about 1 month ago - Stars: 3 - Forks: 1

interactivereport/cellxgene_VIP

Enables cellxgene to generate violin, stacked violin, stacked bar, heatmap, volcano, embedding, dot, track, density, 2D density, sankey and dual-gene plot in high-resolution SVG/PNG format. It also performs differential gene expression analysis and provides a Command Line Interface (CLI) for advanced users to perform analysis using python and R.

Language: HTML - Size: 119 MB - Last synced: 2 months ago - Pushed: 2 months ago - Stars: 117 - Forks: 40

gozsari/Single-Cell-Data-Analysis

Notes and studies about single-cell RNA-Seq analysis

Language: Python - Size: 9.44 MB - Last synced: 3 days ago - Pushed: almost 2 years ago - Stars: 4 - Forks: 2

noamteyssier/adpbulk

pseudobulking on an AnnData object

Language: Python - Size: 19.5 KB - Last synced: 12 days ago - Pushed: 11 months ago - Stars: 19 - Forks: 1

zhanghao-njmu/SCP

An end-to-end Single-Cell Pipeline designed to facilitate comprehensive analysis and exploration of single-cell data.

Language: R - Size: 788 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 284 - Forks: 54

Nuwa-genomics/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 431 MB - Last synced: about 2 months ago - Pushed: about 2 months ago - Stars: 0 - Forks: 0

ch1ru/Nuwa

A bioinformatics web app for single cell RNA seq analysis.

Language: Python - Size: 429 MB - Last synced: 3 months ago - Pushed: 3 months ago - Stars: 0 - Forks: 0

NKI-CCB/sobolev_alignment

Sobolev alignment of deep probabilistic models for comparing single cell profiles

Language: Python - Size: 3.76 MB - Last synced: 2 days ago - Pushed: 3 days ago - Stars: 5 - Forks: 2

Iwo-K/genespector

Language: Python - Size: 4.65 MB - Last synced: 5 months ago - Pushed: almost 2 years ago - Stars: 2 - Forks: 1

mcrewcow/BaranovLab

Main projects during my current position in Petr Baranov Lab | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Language: Jupyter Notebook - Size: 64.9 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 1

kullrich/orthomap 📦

orthomap is a python package to extract orthologous maps (in other words the evolutionary age of a given orthologous group) from OrthoFinder/eggNOG results. Orthomap results (gene ages per orthogroup) can be further used to calculate weigthed expression data (transcriptome evolutionary index) from scRNA sequencing objects.

Language: Python - Size: 59.1 MB - Last synced: 18 days ago - Pushed: 6 months ago - Stars: 6 - Forks: 1

liekevandehaar/Dev_Hb_mouse

Transcriptomic analysis of the developing mouse habenula

Language: Jupyter Notebook - Size: 57.4 MB - Last synced: 7 months ago - Pushed: over 1 year ago - Stars: 2 - Forks: 0

stefanie-baerthel/combinatorial_treatment_analysis

KRAS-mutant pancreatic ductal adenocarcinoma (PDAC) is highly immunosuppressive and resistant to targeted therapies, immune checkpoint blockade and engineered T cells. In this study, we performed a systematic high throughput combinatorial drug screen and identified a synergistic interaction between the MEK inhibitor trametinib and the multi- kinase inhibitor nintedanib. Using single cell RNA sequencing and immunophenotyping, we show that the combination therapy reprograms the immunosuppressive microenvironment and primes cytotoxic and memory T cells to infiltrate the tumors, thereby sensitizing mesenchymal PDAC to PD-L1 inhibition.

Language: Jupyter Notebook - Size: 70.7 MB - Last synced: 7 months ago - Pushed: over 2 years ago - Stars: 1 - Forks: 0

m1ma0314/CSE185Group16_TeeSnee

TeeSnee is an algorithm designed to take high-dimensional gene expression data and represent it in low-dimensional space.

Language: Jupyter Notebook - Size: 1.36 MB - Last synced: 7 months ago - Pushed: 11 months ago - Stars: 0 - Forks: 1

karan-nanda/SquidPy

Explore spatial organization of a mouse brain coronal section with Scanpy and Squidpy in this GitHub repository. Analyze cell interactions, visualize distributions, and uncover patterns using various data exploration and spatial analysis techniques.

Language: Jupyter Notebook - Size: 15.5 MB - Last synced: 4 months ago - Pushed: 9 months ago - Stars: 0 - Forks: 0

karan-nanda/Spatial-RNA-Analysis

This project employs Scanpy in Python for analyzing spatial transcriptomics data, encompassing preprocessing, quality control, clustering, and marker gene identification, resulting in informative visualizations to reveal gene expression patterns and cellular interactions within tissue samples.

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theislab/scanpy-demo-czbiohub

single-cell scanpy teaching

Language: HTML - Size: 9.82 MB - Last synced: 9 months ago - Pushed: over 4 years ago - Stars: 5 - Forks: 4

mcrewcow/Pan_et_al_DFChen_IGFPL1_paper

IGFBPL1 Retinal Microglia Project | Dong Feng Chen Lab collaboration | Schepens Eye Research Institute, Mass General Hospital, Harvard Medical School

Language: Jupyter Notebook - Size: 21.1 MB - Last synced: 10 months ago - Pushed: 10 months ago - Stars: 0 - Forks: 1

KyriakosPsa/BreastCancer-sc

Replication and extension of the single cell RNA-seq analysis paper "Single-cell RNA-seq enables comprehensive tumour and immune cell profiling in primary breast cancer"

Language: Jupyter Notebook - Size: 142 MB - Last synced: 11 months ago - Pushed: 11 months ago - Stars: 1 - Forks: 0

theislab/HPA_reproducibility

Reproducible code for the scRNA-seq analyses in the paper 'The neuroendocrine response to stress at single-cell resolution" by Lopez et al. 2020.

Language: Jupyter Notebook - Size: 120 MB - Last synced: 9 months ago - Pushed: over 3 years ago - Stars: 2 - Forks: 0

mcrewcow/Yizhen_microglia

collab | DFC

Language: Jupyter Notebook - Size: 4.83 MB - Last synced: 12 months ago - Pushed: 12 months ago - Stars: 0 - Forks: 0

Cai-Lab-at-University-of-Michigan/MiCV

MiCV is a python dash-based web-application that enables researchers to upload raw scRNA-seq data and perform filtering, analysis, and manual annotation.

Language: CSS - Size: 9.3 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 5 - Forks: 1

mcrewcow/Sun_Ye_microglia_macrophages_paper

Socs3/Spp1 Project on Microglia in OIR | Ye Sun Lab Collaboration Project | Boston Children's Hospital

Language: Jupyter Notebook - Size: 9.85 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 0 - Forks: 1

ebi-gene-expression-group/scanpy-workflow

Workflow leveraging the scanpy-scripts package to run Scanpy in a Nextflow workflow

Language: Nextflow - Size: 53.7 KB - Last synced: about 1 month ago - Pushed: about 5 years ago - Stars: 6 - Forks: 1

PMBio/mudatasets

Multimodal datasets, in MuData format

Language: Python - Size: 66.4 KB - Last synced: 26 days ago - Pushed: over 1 year ago - Stars: 3 - Forks: 1

SindiLab/ACTINN-PyTorch

An easy-to-use PyTorch implementation of Automatic Cell-Types Identification of single-cell RNA sequencing using Neural Networks (ACTINN)

Language: Python - Size: 44.5 MB - Last synced: about 1 year ago - Pushed: over 1 year ago - Stars: 4 - Forks: 3

poloarol/scrna-analysis-tutorials

scRNA Analysis tutorials

Language: HTML - Size: 8.54 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 0 - Forks: 0

Harsheen98/scRNA-seq-CWGPM-22

scRNA-seq data analysis using scanpy

Language: Jupyter Notebook - Size: 15.7 MB - Last synced: 12 months ago - Pushed: over 1 year ago - Stars: 1 - Forks: 1

buettnerlab/pytometry_legacy

This repository extends scanpy to handle flow and mass cytometry data.

Language: Jupyter Notebook - Size: 282 MB - Last synced: about 1 year ago - Pushed: almost 2 years ago - Stars: 9 - Forks: 1

XpChen79/single-cell-sequence

Language: Jupyter Notebook - Size: 29.3 MB - Last synced: about 1 year ago - Pushed: about 1 year ago - Stars: 0 - Forks: 0

gambalab/scRNAseq_chapter

Review on Single Cell RNA-sequencing

Size: 17.1 MB - Last synced: 12 months ago - Pushed: about 3 years ago - Stars: 1 - Forks: 2

luglilab/SP025_Analysis

Integration analysis with Scanpy and scRNAseq TME from blueprint

Language: Jupyter Notebook - Size: 255 MB - Last synced: 7 months ago - Pushed: 7 months ago - Stars: 1 - Forks: 0

milescsmith/s2a

Seurat to AnnData conversion

Language: Python - Size: 5.58 MB - Last synced: 5 months ago - Pushed: 5 months ago - Stars: 1 - Forks: 0

FASTGenomics/fgread-py

Python readers for different data formats for FASTGenomics.

Language: Python - Size: 107 KB - Last synced: 2 days ago - Pushed: almost 3 years ago - Stars: 1 - Forks: 0

Accio/analysing-scRNAseq-with-scanpy-and-besca

We explore how to use scanpy and besca to analyse single-cell sequencing data

Language: Jupyter Notebook - Size: 11 MB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

FASTGenomics/analysis_empty_scanpy_rpy2

Advanced scanpy environment with R support (rpy2)

Language: Jupyter Notebook - Size: 31.3 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0

FASTGenomics/analysis_empty_scanpy

Language: Jupyter Notebook - Size: 25.4 KB - Last synced: about 1 year ago - Pushed: almost 4 years ago - Stars: 0 - Forks: 0