beigelk

bulkrnaseq_deseq2

Generalized script for DESeq2 analysis of gene counts matrix from nf-core/rnaseq pipeline

code_snippets

Repo for small bits of functional code. Mostly for personal reference or for things I need to use frequently/don't want to forget.

DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

figures_in_R

Code chunks for generating different figures in R.

microscopy

Repo for code related to handling microscopy imaging files (CZI, OME-TIFF)

Nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

rna_velocity_basic

Basic RNA velocity analysis using velocyto (spliced/unspliced counts), Seurat (to get UMAP coords and other metadata), and scVelo (RNA velocity analysis and figures)

scProportionTest

Nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

nichenetr

NicheNet: predict active ligand-target links between interacting cells

beigelk/figures_in_R

Code chunks for generating different figures in R.

beigelk/bulkrnaseq_deseq2

Generalized script for DESeq2 analysis of gene counts matrix from nf-core/rnaseq pipeline

beigelk/code_snippets

Repo for small bits of functional code. Mostly for personal reference or for things I need to use frequently/don't want to forget.

beigelk/DoubletFinder

R package for detecting doublets in single-cell RNA sequencing data

beigelk/microscopy

Repo for code related to handling microscopy imaging files (CZI, OME-TIFF)

beigelk/Nebulosa

R package to visualize gene expression data based on weighted kernel density estimation

beigelk/rna_velocity_basic

Basic RNA velocity analysis using velocyto (spliced/unspliced counts), Seurat (to get UMAP coords and other metadata), and scVelo (RNA velocity analysis and figures)

beigelk/scProportionTest