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Bioinformatics
Scopus
ISSN 1367-4803 · Oxford University Press · 59 artikel di indeks
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Artikel Jurnal Teks lengkap
CoverM: read alignment statistics for metagenomics
SUMMARY: Genome-centric analysis of metagenomic samples is a powerful method for understanding the function of microbial communities. Calculating read coverage is a central part of analysis, enabling differential coverage binning for recovery of genomes and estimation of microbial community…
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ADMET-AI: a machine learning ADMET platform for evaluation of large-scale chemical libraries
MOTIVATION: The emergence of large chemical repositories and combinatorial chemical spaces, coupled with high-throughput docking and generative AI, have greatly expanded the chemical diversity of small molecules for drug discovery. Selecting compounds for experimental validation requires filtering…
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Protein-to-genome alignment with miniprot
MOTIVATION: Protein-to-genome alignment is critical to annotating genes in non-model organisms. While there are a few tools for this purpose, all of them were developed over 10 years ago and did not incorporate the latest advances in alignment algorithms. They are inefficient and could not keep up…
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ggpicrust2: an R package for PICRUSt2 predicted functional profile analysis and visualization
SUMMARY: Microbiome research is now moving beyond the compositional analysis of microbial taxa in a sample. Increasing evidence from large human microbiome studies suggests that functional consequences of changes in the intestinal microbiome may provide more power for studying their impact on…
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compleasm: a faster and more accurate reimplementation of BUSCO
MOTIVATION: Evaluating the gene completeness is critical to measuring the quality of a genome assembly. An incomplete assembly can lead to errors in gene predictions, annotation, and other downstream analyses. Benchmarking Universal Single-Copy Orthologs (BUSCO) is a widely used tool for assessing…
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NanoPack2: population-scale evaluation of long-read sequencing data
SUMMARY: Increases in the cohort size in long-read sequencing projects necessitate more efficient software for quality assessment and processing of sequencing data from Oxford Nanopore Technologies and Pacific Biosciences. Here, we describe novel tools for summarizing experiments, filtering…
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microbiomeMarker: an R/Bioconductor package for microbiome marker identification and visualization
SUMMARY: Characterizing biomarkers based on microbiome profiles has great potential for translational medicine and precision medicine. Here, we present microbiomeMarker, an R/Bioconductor package implementing commonly used normalization and differential analysis (DA) methods, and three supervised…
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propeller: testing for differences in cell type proportions in single cell data
MOTIVATION: Single cell RNA-Sequencing (scRNA-seq) has rapidly gained popularity over the last few years for profiling the transcriptomes of thousands to millions of single cells. This technology is now being used to analyse experiments with complex designs including biological replication. One…
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Annotation of biologically relevant ligands in UniProtKB using ChEBI
MOTIVATION: To provide high quality, computationally tractable annotation of binding sites for biologically relevant (cognate) ligands in UniProtKB using the chemical ontology ChEBI (Chemical Entities of Biological Interest), to better support efforts to study and predict functionally relevant…
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plotsr: visualizing structural similarities and rearrangements between multiple genomes
SUMMARY: Third-generation genome sequencing technologies have led to a sharp increase in the number of high-quality genome assemblies. This allows the comparison of multiple assembled genomes of individual species and demands new tools for visualizing their structural properties. Here, we present…
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YaHS: yet another Hi-C scaffolding tool
SUMMARY: We present YaHS, a user-friendly command-line tool for the construction of chromosome-scale scaffolds from Hi-C data. It can be run with a single-line command, requires minimal input from users (an assembly file and an alignment file) which is compatible with similar tools and provides…
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Gfastats: conversion, evaluation and manipulation of genome sequences using assembly graphs
MOTIVATION: With the current pace at which reference genomes are being produced, the availability of tools that can reliably and efficiently generate genome assembly summary statistics has become critical. Additionally, with the emergence of new algorithms and data types, tools that can improve the…
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GSEApy: a comprehensive package for performing gene set enrichment analysis in Python
MOTIVATION: Gene set enrichment analysis (GSEA) is a commonly used algorithm for characterizing gene expression changes. However, the currently available tools used to perform GSEA have a limited ability to analyze large datasets, which is particularly problematic for the analysis of single-cell…
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Analysing high-throughput sequencing data in Python with HTSeq 2.0
SUMMARY: HTSeq 2.0 provides a more extensive application programming interface including a new representation for sparse genomic data, enhancements for htseq-count to suit single-cell omics, a new script for data using cell and molecular barcodes, improved documentation, testing and deployment, bug…
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GTDB-Tk v2: memory friendly classification with the genome taxonomy database
SUMMARY: The Genome Taxonomy Database (GTDB) and associated taxonomic classification toolkit (GTDB-Tk) have been widely adopted by the microbiology community. However, the growing size of the GTDB bacterial reference tree has resulted in GTDB-Tk requiring substantial amounts of memory (∼320 GB)…
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ProteinBERT: a universal deep-learning model of protein sequence and function
SUMMARY: Self-supervised deep language modeling has shown unprecedented success across natural language tasks, and has recently been repurposed to biological sequences. However, existing models and pretraining methods are designed and optimized for text analysis. We introduce ProteinBERT, a deep…
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ggtranscript : an R package for the visualization and interpretation of transcript isoforms using ggplot2
MOTIVATION: The advent of long-read sequencing technologies has increased demand for the visualization and interpretation of transcripts. However, tools that perform such visualizations remain inflexible and lack the ability to easily identify differences between transcript structures. Here, we…
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Pharokka: a fast scalable bacteriophage annotation tool
SUMMARY: In recent years, there has been an increasing interest in bacteriophages, which has led to growing numbers of bacteriophage genomic sequences becoming available. Consequently, there is a need for a rapid and consistent genomic annotation tool dedicated for bacteriophages. Existing tools…
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igv.js: an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV)
SUMMARY: igv.js is an embeddable JavaScript implementation of the Integrative Genomics Viewer (IGV). It can be easily dropped into any web page with a single line of code and has no external dependencies. The viewer runs completely in the web browser, with no backend server and no data…
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sAMPpred-GAT: prediction of antimicrobial peptide by graph attention network and predicted peptide structure
MOTIVATION: Antimicrobial peptides (AMPs) are essential components of therapeutic peptides for innate immunity. Researchers have developed several computational methods to predict the potential AMPs from many candidate peptides. With the development of artificial intelligent techniques, the protein…