sashielvagus/Multimodal-Deconvolution-of-Zebrafish-Gene-Expression-Using-MuSiC-Project

Multimodal project: MuSiC used to process gene expression data using a signature matrix built from single-cell RNA-seq data that defines gene profiles for each cell type. The goal of this project is to use multimodal to quantify how environmental exposures alter gene expression in zebrafish.

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dputhier/scigenex

This repository stores the scigenex R library.

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dmkv1/scrnaxus

NextFlow pipeline for automated scRNAseq analysis

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LouisFaure/scFates

a scalable python suite for tree inference and advanced pseudotime analysis from scRNAseq data.

Language: Python - Size: 76.1 MB - Last synced at: 15 days ago - Pushed at: about 2 months ago - Stars: 54 - Forks: 4

ankitbioinfo/nico_tutorial

A package that performs cell type annotations on single cell resolution of spatial transcriptomics data, find the niche interactions and covariation patterns between interacted cell types.

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Qile0317/APackOfTheClones

Visualize clonal expansion via circle-packing. 'APackOfTheClones' extends 'scRepertoire' to produce a publication-ready visualization of clonal expansion at a single cell resolution, by representing expanded clones as differently sized circles.

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ATpoint/sc_preprocess

Preprocessing of UMI-based scRNA-seq supporting spliced/unspliced count generation and feature barcoding experiments with salmon-alevin

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crazyhottommy/scclusteval

Single Cell Cluster Evaluation

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bodegalab/irescue

Uncertainty-aware quantification of Transposable Elements expression in scRNA-seq

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AlicenJoyHenning/DamageToolReviewArticle

🗒️ Analysis scripts for the methods outlined in our review article evaluating scRNA-seq damaged cell detection strategies

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asmagen/robustSingleCell

Robust single cell clustering and comparison of population compositions across tissues and experimental models via similarity analysis.

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BaderLab/scClustViz

Explore and share your scRNAseq clustering results

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WT215/bayNorm

Normalization for single cell RNA-seq data

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thelovelab/fishpond

Differential expression and allelic analysis, nonparametric statistics

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theislab/kBET

An R package to test for batch effects in high-dimensional single-cell RNA sequencing data.

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guokai8/scGSVA

scGSVA: Perform GSVA for single cell RNA seq

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wheaton5/souporcell

Clustering scRNAseq by genotypes

Language: Python - Size: 1.66 MB - Last synced at: 6 months ago - Pushed at: 6 months ago - Stars: 168 - Forks: 46

arogozhnikov/demuxalot

Reliable, scalable, efficient demultiplexing for single-cell RNA sequencing

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IMB-Computational-Genomics-Lab/ascend

R package - Analysis of Single Cell Expression, Normalisation and Differential expression (ascend)

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Perik-Zavodskii/2ndDerivativeFeatures

Second Derivative-based selection of VariableFeatures

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iMM-Workshops/2024_Hitchhiker_Guide_scRNA-seq

The Hitchhiker's Guide to scRNA-seq - 2024

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luglilab/SP025_Analysis

Integration analysis with Scanpy and scRNAseq TME from blueprint

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fentouxungui/Fly-Midgut-EEs-scRNAseq 📦

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zavolanlab/SCUREL

Method to detect 3'UTR changes from scRNA-seq

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JiaxuanYang1204/CellScripter

Automated scRNAseq analysis package

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JuliaSingleCellOmics/SnowyOwl.jl

A single-cell RNA sequencing data analysis toolkit in Julia.

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phipsonlab/NextClone

Nextflow pipeline for extracting and counting clonal barcodes

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phipsonlab/CloneDetective

R Package for interrogating clonal data

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JulianSpagnuolo/adtseq

adtseq provides simple Rcpp methods to identify Antibody-Derived-Tags in single cell CITE/REAP-seq data

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NMikolajewicz/scMiko

R package developed for single-cell RNA-seq analysis. It was designed using the Seurat framework, and offers existing and novel single-cell analytic work flows.

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Dragonmasterx87/Interactive-3D-Plotting-in-Seurat-3.0.0

This repository contains R code, with which you can create 3D UMAP and tSNE plots of Seurat analyzed scRNAseq data

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hansolo-bioinfo/scGEM

Discovers nested gene co-expressing modules

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ComunidadBioInfo/cdsb2021_scRNAseq

Taller de la CDSB 2021 sobre análisis de datos de scRNA-seq con Bioconductor

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jianhong/scRNAseqAppBioc2023Workshop

Package demo for scRNAseqApp

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FelixTheStudent/cellpypes

Cell type pipes for R

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hmbaghdassarian/STAT4_v2

scRNAseq analysis for STAT4 variants

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waiman-chan/engle_hcfp_nature-genetics_2023-05

final code used in HCPF paper

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elolab/Totem-protocol

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JuliaSingleCellOmics/OmicsProfiles.jl

A data structure for single cell sequencing data analysis in Julia.

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marchinilab/dropsim

R Package for Single Cell RNAseq Synthetic Data Simulation

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zifornd/chromium

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milescsmith/SeuratPlotly

Plot_ly-based plotting functions for use with Seurat objects

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Hattyoriiiiiii/single-cell-scripts

scripts for scRNA-Seq/scATAC-Seq

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Dragonmasterx87/Merging-multiple-Seurat-Objects

Hello there! Some code on how to merge >2 Seurat objects and maintain object identity :)

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ComunidadBioInfo/minicurso_mayo_2021

Este es el material del mini curso "Exploración interactiva de datos: plotly y iSEE" ofrecido por la Red Mexicana de Bioinformática y la Comunidad de Desarrolladores de Software en Bioinformática.

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rahulbhadani/scomix

Single-Cell Data Science

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asmagen/hierarchicalSingleCell

An R package to robustly identify subpopulations in single-cell RNASeq data.

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lcolladotor/osca_LIIGH_UNAM_2020

Course for LCG-UNAM at LIIGH-UNAM for March 2020 based on the book "Orchestrating Single Cell Analysis with Bioconductor" and WEHI's scRNA-seq course

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eisascience/scRNASeq_old

Tools and functions for conducting scRNASeq in my pipelines

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