Geo Pertea

stringtie. Transcript assembly and quantification for RNA-Seq

gffread. GFF/GTF utility providing format conversions, region filtering, FASTA sequence extraction and more

gffcompare. classify, merge, tracking and annotation of GFF files by comparing to a reference annotation GFF

gclib. GCLib - Genomic C++ library of reusable code for bioinformatics projects

cdbfasta. Constant DataBase tools for indexing and retrieving records from multi-FASTA or similarly structured files

gsrc. various sources and scripts for genomic research software

gscripts. mish-mash of scripts I have been using in genomics (bioinformatics) or IT/engineering

mgblast. fast all-vs-all DNA alignment tool, modification of megablast from a 2006 version of NCBI C Toolkit

tiebrush. summarize and filter read alignments from multiple sequencing samples (taken as sorted BAM files)

bamread. basic SAM/BAM/CRAM file reading/writing (and C++ wrapper classes) using HTSlib API

fqtrim. filtering and trimming next generation sequencing reads

jquery-heatmap. Simple Heatmap plugin for jquery

CuffCompare. compare results and evaluate the accuracy of RNA-Seq transcript assemblers (Cufflinks, Stringtie)

pwasm. MSA and consensus (assembly) generator from pairwise alignments of DNA sequences

Rgffcmp. playing with gffcompare data in R

scRNAutils. Utility scripts and notebooks for learning scRNA-Seq data processing

ggtranscript. Visualising transcript structure and annotation using ggplot2

mblasm. consensus (assembly) generator from mgblast (modified megablast) pairwise alignments

gsegindex. Testing genomic segment index for fast intersection queries

ChatGPTServerCommander. This project is a server that exposes terminal commands and file editing functionality as an API for ChatGPT Actions. In essence, it allows you to control any machine where you install this with ChatGPT. Install, run, and edit anything, even itself.

AutomaticReviewGeneration. Automatic Review Generation Method with LLMs

storm. An LLM-powered knowledge curation system that researches a topic and generates a full-length report with citations.

CNView. CNView wrapper

trmap. mass transcript classification by streaming GFF/BED over reference GFF/BED

tensorQTL_R. R-based workflow to prep data for tensorQTL