Antônio Camargo

genomad. geNomad: Identification of mobile genetic elements

typst-skills. Agent skills that guide AI agents to write Typst code

taxopy. A Python package for obtaining complete lineages and the lowest common ancestor (LCA) from a set of taxonomic identifiers

RNAsamba. A tool for computing the coding potential of RNA transcript sequences using deep learning classification model

prodigal-gv. A fork of Prodigal meant to improve gene calling for giant viruses and viruses that use alternative genetic codes

tspex. tspex: tissue-specificity calculator

ictv-mmseqs2-protein-database. Python

magpurify2. Identify and remove contaminants from metagenome-assembled genomes

genotypst. genotypst: A bioinformatics Typst package for bioinformatics data analysis and visualization

polars-pairing. Plugin that provides pairing functions to the Polars library

pydustmasker. Python library for identification and masking of low-complexity regions in nucleotide sequences

seq-hasher. Compute hash digests for DNA sequences in a FASTA file

pycoverm. Simple Python interface to CoverM's fast coverage estimation functions

pyleiden. A CLI tool for clustering with the Leiden algorithm

reorient-circular-seq. Reorient circular DNA sequences to prevent gene truncation at the edges

kcounter. A simple package for counting DNA k-mers in Python. Written in Rust.

polars-fastx. A Polars plugin for parsing FASTA and FASTQ files into DataFrames

tr-trimmer. Identify and trim terminal repeats from sequences in FASTA files

cluster-msa. Python

diversify-pfam. Python

local-cd-search. Protein annotation using local PSSM databases from CDD

WillItCode. Compute the coding potential of RNA sequences

parallel-prodigal. Python

2022-pths-rna-seq-analysis. RNA-Seq analysis for "Transcription Factor 4 loss-of-function is associated with deficits in progenitor proliferation and cortical neuron content"

bioinformatics-snakemake-pipelines. Collection of Snakemake pipeline for commin bioinformatics tasks

retrieve-logan-contigs. Downloads contigs from a specified Logan assembly

retrieve-ena-metadata. Retrieve and parse metadata retrieved from the ENA

cortical-organoids-reanalysis. Reanalysis of the "cortical.organoids" dataset from "Complex Oscillatory Waves Emerging from Cortical Organoids Model Early Human Brain Network Development"

genomad-annotate-module-snakemake. A snakemake workflow implementing the genomad annotate module steps

taxonkit. A Practical and Efficient NCBI Taxonomy Toolkit

pyrodigal-gv. A Pyrodigal extension to predict genes in giant viruses and viruses with alternative genetic code.

InSilicoSeq. :rocket: A sequencing simulator