XpBrew, an end-to-end Python workflow that was applied to generate PanXpresso, a comprehensive collection of gene expression datasets covering the taxonomic breadth of plants, animals, fungi, bacteria and archaea is introduced.
Abstract
Rapid developments in sequencing technologies have reduced the costs of transcriptomic experiments and resulted in a plethora of publicly available RNA-seq datasets. This is a valuable resource that can be harnessed to obtain novel biological insights through data upcycling. In this wake, we introduce XpBrew, an end-to-end Python workflow that was applied to generate PanXpresso, a comprehensive collection of gene expression datasets covering the taxonomic breadth of plants, animals, fungi, bacteria and archaea. XpBrew (https://github.com/PuckerLab/XpBrew) and PanXpresso (https://doi.org/10.60507/FK2/OBIGQH) are freely available.
RNA-Seq, analyses of RNA abundance by next-generation sequencing, has become a near-universal tool in modern biology. Availability of streamlined protocols and kits, straightforward ability to multiplex hundreds of samples, low cost of short-read sequencing, and well-established analytical pipelines make RNA-Seq a meth...
Dustin R. Fetch, Alexey A. Soshnev· bioRxiv· 1 citation
Summary Current tools for RNA epitranscriptomic modification and structural feature analysis are often fragmented, focusing on single signal types and struggling with processing efficiency, especially as sequencing data volumes increase and single-cell technologies advance. To address this challenge, we developed Modte...
Tong Zhou, Yifan Hong, Panfeng Li et al.· bioRxiv· 1 citation
Reproducible high-performance computing pipelines for transcriptomic analysis are essential for population-scale precision oncology, yet most published workflows address only a single sequencing modality or lack benchmarking on underrepresented populations. We present KazRNA-Pipe, an open-source Nextflow v26.04.6 workf...
M. Ashimgaliyev, Beimbet Daribayev, A. Zhumadillayeva et al.· BioMedInformatics· 0 citations
Motivation Single-cell RNA sequencing (scRNA-seq) cluster annotation is a critical step in data analysis. Current methods are time-consuming, difficult to reproduce, or limited in tissue or species coverage. Results We developed celltypeEnrich, a cluster-level annotation tool that uses a hypergeometric test to identify...
Samuel D. Rutledge, G. Tuteja· bioRxiv· 0 citations
FEDKEA, an enzyme annotation tool leveraging protein language models, and a user-friendly, FEDKEA-based metagenomic pipeline, MEnzMap, which encompasses the entire analysis workflow—from raw data quality control to function prediction and downstream analyses are designed.
Lei Zheng, Bowen Li, Siqi Xu et al.· Science Advances· 0 citations
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