vertesy Goto Github PK

acm.tomoseq

Analysis scripts for the manuscript: "Spatial transcriptomics unveils ZBTB11 as a regulator of cardiomyocyte degeneration in arrhythmogenic cardiomyopathy".

awesome-single-cell

List of software packages for single-cell data analysis, including RNA-seq, ATAC-seq, etc.

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.

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.

defense

Abel's Phd Defense & party on 19.04.2018 (periodically updated)

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.

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. "

limited.stress.in.brain.organoids

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

markdownhelpers

Helper functions (control and parsing) for MarkdownReports and ggExpress

markdownreports

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

markdownreports.v2.9.5

Legacy version (v2.9.5) of MarkdownReports for backward compatibility

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).

persian-words-frequency

Persian Words Frequency - A collection of words frequency lists for Persian text corpora

pseudobulk

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

readwriter

Functions to read and write tabular data files conveniently. Complements CodeAndRoll2.

rocinante

A collection of custom R functions. Helper functions complementing CodeAndRoll2.

roxygenready

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

scg

scg.01

SCG.01

scphaser

R package for haplotype phasing using single-cell RNA-seq data

seurat.cbe.issues

Issue tracker repo for running Seurat on CLIP/CBE

seurat.multicore

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

seurat.pipeline

Seurat Pipeline using the Seurat.utils package