Beast code in Giters

Geo Pertea's repositories

gffread

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

Language:C++MIT350 9 128

stringtie

Transcript assembly and quantification for RNA-Seq

Language:C++MIT348 28 414

gffcompare

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

Language:C++MIT180 14 85

gclib

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

Language:C++NOASSERTION32 4 8

cdbfasta

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

Language:C++8 1 2

gscripts

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

Language:PerlUnlicense6 1 1

bamread

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

Language:C++4 20

ggtranscript

Visualising transcript structure and annotation using ggplot2

Language:R100

chatgpt-your-files

Production-ready MVP for securely chatting with your documents using pgvector

000

clview

ACE dna sequence cluster viewer

Language:C++000

fastp

An ultra-fast all-in-one FASTQ preprocessor (QC/adapters/trimming/filtering/splitting/merging...)

Language:C++MIT000

gfstlib

fast multi-threaded serialization of tabular data (fstlib) adapted for genomics use cases

MPL-2.0000

GPTvecdb

example to make and query embeddings from a custom set of documents

000

gtex-pipeline

GTEx & TOPMed data production and analysis pipelines

BSD-3-Clause000

htslib

C library for high-throughput sequencing data formats

Language:CNOASSERTION010

openai-cookbook

Examples and guides for using the OpenAI API

MIT000

PowerRangesR

GenomicRanges workbook - the power of GRanges

Language:R010

pygmailon

test/cleanup Gmail Inbox using GMail API

Language:Python020

quivr

🧠 Dump all your files and chat with it using your Generative AI Second Brain using LLMs ( GPT 3.5/4, Private, Anthropic, VertexAI ) & Embeddings 🧠

Language:TypeScriptApache-2.0000

r-dte

Differential Transcript Expression in R

Language:R000

R_data_table

experimenting with R data.table

000

r_delarray

DelayedArray data in SummarizedExperiment

Language:R020

react101

react intro

Language:JavaScript000

regtools

Integrate DNA-seq and RNA-seq data to identify mutations that are associated with regulatory effects on gene expression.

Language:C++MIT010

rnaseqc

Fast, efficient RNA-Seq metrics for quality control and process optimization

Language:C++NOASSERTION000

samcounts

report feature counts and read mapping stats for RNA-Seq alignment data

MIT020

SPIT

DTU analysis tool

Language:Jupyter NotebookGPL-3.0010

strgmix_plots

some plots and scripts for the stringtie hybrid paper

Language:Python000

svgs

SVG clip art for web, presentations etc.

020

tensorQTL_R

R-based workflow to prep data for tensorQTL

Language:Jupyter Notebook020