Abel Vertesy's Projects
Analysis scripts for the manuscript: "Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy".
List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.
Analysis scripts for the Ebbing et manuscript: "Spatially-resolved transcriptomics in C. elegans identifies sex-specific differences in gene expression patterns"
A collection of custom R functions. Works with MarkdownReports, SeuratUtils but also as a standalone set of more than 200 productivity tools.
A set of more than >130 productivity functions: vector, matrix, list manipulations and math. Used by MarkdownReports, ggExpress, SeuratUtils, etc.
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.
Store (smaller) data objects in your R code - make your script fully reproducable yet easily sharable.
Abel's Phd Defense & party on 19.04.2018 (periodically updated)
Practical programming skills to analyze and visualize data
ggExpress is the fastest way to create, annotate and and save plots in R.
The single-cell analysis code for Bajaj 2020
Tools to work with isolated environments for in-memory pipelines in R.
Analysis scripts for the manuscript "Spindle checkpoint silencing at kinetochores at submaximal microtubule occupancy" by Etemad et al. "
Analysis for Vertesy et al., "Gruffi removes stressed cells from brain organoid datasets"
Helper functions (control and parsing) for MarkdownReports and ggExpress
Type Less, Plot More. Create (scientific) plots with very little code and write (markdown) reports easily from your R scripts
Legacy version (v2.9.5) of MarkdownReports for backward compatibility
MarkdownReports Development repo for v4++. See "MarkdownReports" repo for v3.1.1 (stable)
Functions and wrappers to manage R packages (creation, documentation, dependencies, checks).
Persian Words Frequency - A collection of words frequency lists for Persian text corpora
Cluster-specific pseudo-bulk analysis of 10X single-cell RNA-seq data by connecting Seurat to the VBC RNA-seq pipeline.
Functions to read and write tabular data files conveniently. Complements CodeAndRoll2.
A collection of custom R functions. Helper functions complementing CodeAndRoll2.
Prepare your R function library to be compiled into an R package by Roxygen
SCG.01
R package for haplotype phasing using single-cell RNA-seq data
Issue tracker repo for running Seurat on CLIP/CBE
Multicore and utility functions for Seurat 2 & 3, using doMC / foreach packages.
Seurat Pipeline using the Seurat.utils package