Abel Vertesy's repositories
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
pseudoBulk
Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.
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.
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"
CodeAndRoll
A collection of custom R functions. Works with MarkdownReports, SeuratUtils but also as a standalone set of more than 200 productivity tools.
CodeAndRoll2
A set of more than >130 productivity functions: vector, matrix, list manipulations and math. Used by MarkdownReports, ggExpress, SeuratUtils, etc.
Seurat.Pipeline
Seurat Pipeline using the Seurat.utils package
TheCorvinas
Various Scripts and Summaries
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
MarkdownHelpers
Helper functions (control and parsing) for MarkdownReports and ggExpress
ACM.TomoSeq
Analysis scripts for the manuscript: "Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy".
DatabaseLinke.R
A set of functions to parse and open (search query) links to genomics related and other websites for R. Useful when you want to explore e.g.: the function of a set of differentially expressed genes.
DataInCode
Store (smaller) data objects in your R code - make your script fully reproducable yet easily sharable.
InterNeuronMigration
The single-cell analysis code for Bajaj 2020
isoENV
Tools to work with isolated environments for in-memory pipelines in R.
Kinetochore
Analysis scripts for the manuscript "Spindle checkpoint silencing at kinetochores at submaximal microtubule occupancy" by Etemad et al. "
MarkdownReportsDev
MarkdownReports Development repo for v4++. See "MarkdownReports" repo for v3.1.1 (stable)
PackageTools
Functions and wrappers to manage R packages (creation, documentation, dependencies, checks).
ReadWriter
Functions to read and write tabular data files conveniently. Complements CodeAndRoll2.
Single-Cell-Omics-Course
A summer workshop on single-cell (gen)omics and data analysis
single-cell-sequencing
scripts and functions to analyse single-cell sequencing data
slighshot.utils
[Archived] Utility functions for slignshot pseudotime prediction tool for single-cell RNAseq analysis.
Stringendo
String parsing functionalites for generating plotnames, filenames and path. Used by MarkdownReprots and ggExpress
vertesy.github.io
My Github Page