STAR Suite is presented, which extends the STAR aligner into a single executable for transcriptomics processing, adding 132,226 lines of C/C++ made tractable through human-directed AI software engineering.
The results suggest that current coding agents can accelerate scaffolding, documentation, and routine implementation, but they do not eliminate the need for expert review in bioinformatics workflow construction.
Paul R. Munn, Jennifer K. Grenier· bioRxiv· 0 citations
MErlin (Methylation-driven Expression & Regulation Linkage in Interacting Nuclear-domains), a multi-omics toolkit comprising seventeen composable modules, from basecalled modBAM files to ranked gene-level evidence and a self-contained HTML report is presented.
Single-cell RNA sequencing has transformed cell biology by enabling precise transcriptomic measurements of individual cells. The Sequence Read Archive (SRA) is the largest public repository of sequencing reads, yet much of it remains underutilized due to unstandardized metadata. Here, we introduce scBaseCount, a databa...
Nicholas D. Youngblut, Christopher Carpenter, Arshia Nayebnazar et al.· Cell· 5 citations
GEOMeta provides a scalable resource and reproducible framework for metadata curation in the Gene Expression Omnibus, and benchmarked transcriptome representation models for predicting sex, age, tissue and disease from transcriptome embeddings.
Xiaodan Zhang, S. Paithankar, Jing Pu et al.· bioRxiv· 0 citations
FetchPA is an intuitive pipeline which allows users with virtually no scripting and version control experience to install and manage all software for end-to-end analyses of ATAC-Seq data and guides the user through the identification of differentially accessible regions.
Dustin R. Fetch, Alexey A. Soshnev· bioRxiv· 0 citations
KazRNA-Pipe is presented, an open-source Nextflow v26.6 workflow processing both bulk and single-cell RNA sequencing (RNA-seq) within a unified Singularity-containerized environment with graphics processing unit (GPU) acceleration through the RAPIDS ecosystem.
M. Ashimgaliyev, Beimbet Daribayev, A. Zhumadillayeva et al.· BioMedInformatics· 0 citations
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