vertesy/pseudoBulk

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License
MIT License
Created about 5 years ago
Updated about 2 years ago

vertesy/pseudoBulk

vertesy

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Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.

Seurat.utils

Various utility functions for Seurat single-cell analysis

MarkdownReports

Type Less, Plot More. Create (scientific) plots with very little code and write (markdown) reports easily from your R scripts

RoxygenReady

Prepare your R function library to be compiled into an R package by Roxygen

Seurat.multicore

Multicore and utility functions for Seurat 2 & 3, using doMC / foreach packages.

CodeAndRoll

A collection of custom R functions. Works with MarkdownReports, SeuratUtils but also as a standalone set of more than 200 productivity tools.

Seurat.Pipeline

Seurat Pipeline using the Seurat.utils package

TheCorvinas

Various Scripts and Summaries

C.elegans.Spatial.Transcriptomics

Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"

X-Reactivation

Analysis scripts for the Vertesy 2018 paper: "Parental haplotype specific single-cell transcriptomics reveal incomplete epigenetic reprogramming in human female germ cells"

Exploratory-data-analysis-in-R

Practical programming skills to analyze and visualize data

ggExpress

ggExpress is the fastest way to create, annotate and and save plots in R.

Limited.Stress.in.Brain.organoids

Analysis for Vertesy et al., "Gruffi removes stressed cells from brain organoid datasets"

Seurat.CBE.issues

Issue tracker repo for running Seurat on CLIP/CBE