Bulk and single-cell RNA sequencing has become essential for investigating disease mechanisms and identifying diagnostic biomarkers, but the growing volume of transcriptomic data remains difficult to reuse efficiently for many researchers.
Bulk RNA-seq and single-cell RNA-seq (scRNA-seq) are widely used to investigate gene-expression changes, but downstream analysis often requires multiple statistical, visualization, and reporting tools, creating fragmented workflows that are difficult to configure and reproduce. We developed CoTRA (Comprehensive Toolbox...
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
Cytos Multimodal Pooled Screening (CytosMPS) measures CRISPR guide identity, morphology, native 3′ transcriptome, and protein abundance and localization in the same fixed cells. Following IL-1β stimulation, cells with higher nuclear NF-κB show lower phospho-p38/HSP27 and higher NFKBIA/DUSP1 in the same cell, a measurem...
Tyler Lopez, J. Rabalais, Ben Song et al.· bioRxiv· 0 citations
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.
Shakunthala Natarajan, Claudia Sterling, N. Choudhary et al.· bioRxiv· 0 citations
This chapter covers quality control, normalization, sparse data handling, and transcript quantification for both bulk and snRNA-seq, along with strategies to address challenges such as multi-mapped reads and batch effects, and examines how artificial intelligence and machine learning techniques can improve data process...
S. P. Dharshini, Y.-H. Taguchi, M. Gromiha· Methods in molecular biology· 0 citations
Application of scFlowReport to a publicly available Atopic Dermatitis scRNA-seq dataset demonstrated its utility by enabling researchers to obtain complementary biological evidence from multiple established downstream analyses.
Nayoung Park, H. Lee, Jaebum Kim· Biomolecules· 0 citations
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