freeCount: A Coding Free Framework for Guided Count Data Visualization and Analysis

被引：0
作者：
Brooks, Elizabeth M. [1 ]
Sanders, Sheri A. [1 ]
Pfrender, Michael E. [1 ]
机构：
[1] Univ Notre Dame, Notre Dame, IN 46556 USA
来源：
PRACTICE AND EXPERIENCE IN ADVANCED RESEARCH COMPUTING 2024, PEARC 2024 | 2024年
基金：
美国国家科学基金会;
关键词：
R Shiny; Interactive Interfaces; Analysis Framework; Genomics; Transcriptomics; Metagenomics;
D O I：
10.1145/3626203.3670605
中图分类号：
TP3 [计算技术、计算机技术];
学科分类号：
0812 ;
摘要：
The analysis and interpretation of high-dimensional biological data sets is a challenging task. Exploratory data analysis of count data produced by next-generation sequencing technologies presents a common hurdle to researchers. Biologists often find it difficult to get started with the analysis process, which can be time consuming and repetitive. With the freeCount analysis framework students and researchers are guided through the iterative steps of data assessment, processing, and analysis in a visual environment. The freeCount analysis framework takes advantage of the reactive features of R Shiny to deliver a set of modular and interactive tools and tutorials for the structured analysis and visualization of count data.
引用
收藏
页数：4
相关论文
共 46 条
  • [31] Sainsc: A Computational Tool for Segmentation-Free Analysis of In Situ Capture Data
    Mueller-Boetticher, Niklas
    Tiesmeyer, Sebastian
    Eils, Roland
    Ishaque, Naveed
    [J]. SMALL METHODS, 2024,
  • [32] Sparse network modeling and metscape-based visualization methods for the analysis of large-scale metabolomics data
    Basu, Sumanta
    Duren, William
    Evans, Charles R.
    Burant, Charles F.
    Michailidis, George
    Karnovsky, Alla
    [J]. BIOINFORMATICS, 2017, 33 (10) : 1545 - 1553
  • [33] Method of moments framework for differential expression analysis of single-cell RNA sequencing data
    Kim, Min Cheol
    Gate, Rachel
    Lee, David S.
    Tolopko, Andrew
    Lu, Andrew
    Gordon, Erin
    Shifrut, Eric
    Garcia-Nieto, Pablo E.
    Marson, Alexander
    Ntranos, Vasilis
    Ye, Chun Jimmie
    [J]. CELL, 2024, 187 (22) : 6393 - 6410.e16
  • [34] B-CAN: a resource sharing platform to improve the operation, visualization and integrated analysis of TCGA breast cancer data
    Wen, Can-Hong
    Ou, Shao-Min
    Guo, Xiao-Bo
    Liu, Chen-Feng
    Shen, Yan-Bo
    You, Na
    Cai, Wei-Hong
    Shen, Wen-Jun
    Wang, Xue-Qin
    Tan, Hai-Zhu
    [J]. ONCOTARGET, 2017, 8 (65) : 108778 - 108785
  • [35] A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
    Berihu, Maria
    Somera, Tracey S.
    Malik, Assaf
    Medina, Shlomit
    Piombo, Edoardo
    Tal, Ofir
    Cohen, Matan
    Ginatt, Alon
    Ofek-Lalzar, Maya
    Doron-Faigenboim, Adi
    Mazzola, Mark
    Freilich, Shiri
    [J]. MICROBIOME, 2023, 11 (01)
  • [36] A framework for the targeted recruitment of crop-beneficial soil taxa based on network analysis of metagenomics data
    Maria Berihu
    Tracey S. Somera
    Assaf Malik
    Shlomit Medina
    Edoardo Piombo
    Ofir Tal
    Matan Cohen
    Alon Ginatt
    Maya Ofek-Lalzar
    Adi Doron-Faigenboim
    Mark Mazzola
    Shiri Freilich
    [J]. Microbiome, 11
  • [37] Signalling entropy: A novel network-theoretical framework for systems analysis and interpretation of functional omic data
    Teschendorff, Andrew E.
    Sollich, Peter
    Kuehn, Reimer
    [J]. METHODS, 2014, 67 (03) : 282 - 293
  • [38] CoGe LoadExp+: A web-based suite that integrates next-generation sequencing data analysis workflows and visualization
    Grover, Jeffrey W.
    Bomhoff, Matthew
    Davey, Sean
    Gregory, Brian D.
    Mosher, Rebecca A.
    Lyons, Eric
    [J]. PLANT DIRECT, 2017, 1 (02)
  • [39] Imaging Biomarkers and Gene Expression Data Correlation Framework for Lung Cancer Radiogenomics Analysis Based on Deep Learning
    Sui, Dong
    Guo, Maozu
    Ma, Xiaoxuan
    Baptiste, Julian
    Zhang, Lei
    [J]. IEEE ACCESS, 2021, 9 (09): : 125247 - 125257
  • [40] National Human Genome Research Institute Genomic Data Science Analysis, Visualization, and Informatics Lab-Space: Reaching out to Clinicians
    Hall, Jennifer L.
    Honeycutt, Sally
    Gonzalez, Nicole
    O'Donnell-Luria, Anne
    Taylor, Casey Overby
    Stevens, Laura
    Philippakis, Anthony A.
    Schatz, Michael C.
    [J]. CIRCULATION-GENOMIC AND PRECISION MEDICINE, 2023, 16 (03): : 275 - 276
12345