The main bioinformatics analysis is listed by figure The main scripts for scRNAseq are listed as separate folders
A copy of the main scRNAseq object is located in Zendo link:
A copy of the Periodic finder and QuasiIDR finder are stored also: Links:
https://github.com/alexpmagalhaes/PeriodicBlock_finder
https://github.com/gozdekibar/QuasiIDRFinder
Questions regarding code please email:
Alexandre P Magalhaes -> magalhae@molgen.mpg.de or to github: @alexpmagalhaes
R packages needed:
tidyverse, ggthemes, ggpubr, bbplot, circlize, MASS, viridis, cowplot, RColorBrewer, ggrepel, readxl, drawProteins, Biostrings, universalmotif, DESeq2, ComplexHeatmap, dendextend, biomaRt, SARTools, pheatmap, pcaExplorer, topGO, org.Hs.eg.db, tidyverse, cluster, factoextra, NbClust, Seurat, hdf5r, kableExtra, limma, sva, scran, DoubletFinder, gprofiler2, rliger, future, harmony, clustree, venn, enrichR, rafalib, scPred, loomR, SeuratWrappers, velocyto.R, Nebulosa, ggalluvial, patchwork, EnvStats, RcppCNPy, DescTools, rison, seqinr, protr, jsonlite, DOSE, GSEABase
Python packages needed:
velocyto, alphafold, metapredict, pandas, matplotlib, localcider, coolbox, scanpy, anndata, numpy, cellrank , scvelo, igraph, Biopython