Abel Vertesy's repositories
CodeAndRoll2
A set of more than >130 productivity functions: vector, matrix, list manipulations and math. Used by MarkdownReports, ggExpress, SeuratUtils, etc.
Seurat.utils
Various utility functions for Seurat single-cell analysis
Stringendo
String parsing functionalites for generating plotnames, filenames and path. Used by MarkdownReprots and ggExpress
MarkdownReports
Type Less, Plot More. Create (scientific) plots with very little code and write (markdown) reports easily from your R scripts
ReadWriter
Functions to read and write tabular data files conveniently. Complements CodeAndRoll2.
MarkdownHelpers
Helper functions (control and parsing) for MarkdownReports and ggExpress
Seurat.Pipeline
Seurat Pipeline using the Seurat.utils package
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.
TheCorvinas
Various Scripts and Summaries
PackageTools
Functions and wrappers to manage R packages (creation, documentation, dependencies, checks).
isoENV
Tools to work with isolated environments for in-memory pipelines in R.
DataInCode
Store (smaller) data objects in your R code - make your script fully reproducable yet easily sharable.
slighshot.utils
[Archived] Utility functions for slignshot pseudotime prediction tool for single-cell RNAseq analysis.
Limited.Stress.in.Brain.organoids
Analysis for Vertesy et al., "Gruffi removes stressed cells from brain organoid datasets"
ACM.TomoSeq
Analysis scripts for the manuscript: "Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy".
vertesy.github.io
My Github Page
RoxygenReady
Prepare your R function library to be compiled into an R package by Roxygen
MarkdownReportsDev
MarkdownReports Development repo for v4++. See "MarkdownReports" repo for v3.1.1 (stable)
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.CBE.issues
Issue tracker repo for running Seurat on CLIP/CBE
Template
This is a template repo
InterNeuronMigration
The single-cell analysis code for Bajaj 2020
single-cell-sequencing
scripts and functions to analyse single-cell sequencing data
pseudoBulk
Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.
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"
Kinetochore
Analysis scripts for the manuscript "Spindle checkpoint silencing at kinetochores at submaximal microtubule occupancy" by Etemad et al. "
Single-Cell-Omics-Course
A summer workshop on single-cell (gen)omics and data analysis