RNA_SEQ_PIPELINE_2024.Rmd - Details the steps of RNA-Sequencing Analysis from expression matrix to Filtering/Normalization, Differential Expression (EdgeR or , GSEA & WGCNA & many different visualizations.
scRNA_Pipe.R - Single Cell Sequencing Pipeline including filtering, normalization, dimensional reduction, Clustering and Differential Expression Analysis + Trajectory Analysis, etc.
Count_Kmer.py - Run from command line and will return kmer counts for each fasta file in indicated directory.
Prep_fasta_files_for_PAML.py - script to change file names, remove gaps and translate Fasta sequences to prepare to run PAML for evolutionary analysis.
RSeQC.sh - Runs Ribosome Removal program RSeQC on directory of files. (for RNA-Seq)
STAR.sh - Runs star alignment on indicated files. (for RNA-Seq)
remove_seqs_by_length.py - remove fasta files that dont meet certain length.
Find_Stop_Codons.py - Find Sequences with Stop Codons in Open-Reading Frame in Fasta File, returns headers of fasta files with Stop Codons in ORF, run on CLI
2024