BIOMARKERS

Molecular Biopsy of Human Tumors

- a resource for Precision Medicine *

201 related articles for article (PubMed ID: 35392802)

  • 1. FindIT2: an R/Bioconductor package to identify influential transcription factor and targets based on multi-omics data.
    Shang GD; Xu ZG; Wan MC; Wang FX; Wang JW
    BMC Genomics; 2022 Apr; 23(Suppl 1):272. PubMed ID: 35392802
    [TBL] [Abstract][Full Text] [Related]  

  • 2. ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization.
    Yu G; Wang LG; He QY
    Bioinformatics; 2015 Jul; 31(14):2382-3. PubMed ID: 25765347
    [TBL] [Abstract][Full Text] [Related]  

  • 3. ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data.
    Ou J; Liu H; Yu J; Kelliher MA; Castilla LH; Lawson ND; Zhu LJ
    BMC Genomics; 2018 Mar; 19(1):169. PubMed ID: 29490630
    [TBL] [Abstract][Full Text] [Related]  

  • 4. TFEA.ChIP: a tool kit for transcription factor binding site enrichment analysis capitalizing on ChIP-seq datasets.
    Puente-Santamaria L; Wasserman WW; Del Peso L
    Bioinformatics; 2019 Dec; 35(24):5339-5340. PubMed ID: 31347689
    [TBL] [Abstract][Full Text] [Related]  

  • 5. BRGenomics for analyzing high-resolution genomics data in R.
    DeBerardine M
    Bioinformatics; 2023 Jun; 39(6):. PubMed ID: 37208173
    [TBL] [Abstract][Full Text] [Related]  

  • 6. esATAC: an easy-to-use systematic pipeline for ATAC-seq data analysis.
    Wei Z; Zhang W; Fang H; Li Y; Wang X
    Bioinformatics; 2018 Aug; 34(15):2664-2665. PubMed ID: 29522192
    [TBL] [Abstract][Full Text] [Related]  

  • 7. GUIDEseq: a bioconductor package to analyze GUIDE-Seq datasets for CRISPR-Cas nucleases.
    Zhu LJ; Lawrence M; Gupta A; Pagès H; Kucukural A; Garber M; Wolfe SA
    BMC Genomics; 2017 May; 18(1):379. PubMed ID: 28506212
    [TBL] [Abstract][Full Text] [Related]  

  • 8. RIPSeeker: a statistical package for identifying protein-associated transcripts from RIP-seq experiments.
    Li Y; Zhao DY; Greenblatt JF; Zhang Z
    Nucleic Acids Res; 2013 Apr; 41(8):e94. PubMed ID: 23455476
    [TBL] [Abstract][Full Text] [Related]  

  • 9. GenomicDistributions: fast analysis of genomic intervals with Bioconductor.
    Kupkova K; Mosquera JV; Smith JP; Stolarczyk M; Danehy TL; Lawson JT; Xue B; Stubbs JT; LeRoy N; Sheffield NC
    BMC Genomics; 2022 Apr; 23(1):299. PubMed ID: 35413804
    [TBL] [Abstract][Full Text] [Related]  

  • 10. systemPipeR: NGS workflow and report generation environment.
    H Backman TW; Girke T
    BMC Bioinformatics; 2016 Sep; 17():388. PubMed ID: 27650223
    [TBL] [Abstract][Full Text] [Related]  

  • 11. ggcoverage: an R package to visualize and annotate genome coverage for various NGS data.
    Song Y; Wang J
    BMC Bioinformatics; 2023 Aug; 24(1):309. PubMed ID: 37559015
    [TBL] [Abstract][Full Text] [Related]  

  • 12. A protocol for RNA methylation differential analysis with MeRIP-Seq data and exomePeak R/Bioconductor package.
    Meng J; Lu Z; Liu H; Zhang L; Zhang S; Chen Y; Rao MK; Huang Y
    Methods; 2014 Oct; 69(3):274-81. PubMed ID: 24979058
    [TBL] [Abstract][Full Text] [Related]  

  • 13. FunChIP: an R/Bioconductor package for functional classification of ChIP-seq shapes.
    Parodi ACL; Sangalli LM; Vantini S; Amati B; Secchi P; Morelli MJ
    Bioinformatics; 2017 Aug; 33(16):2570-2572. PubMed ID: 28398543
    [TBL] [Abstract][Full Text] [Related]  

  • 14. QuasR: quantification and annotation of short reads in R.
    Gaidatzis D; Lerch A; Hahne F; Stadler MB
    Bioinformatics; 2015 Apr; 31(7):1130-2. PubMed ID: 25417205
    [TBL] [Abstract][Full Text] [Related]  

  • 15. Omics Pipe: a community-based framework for reproducible multi-omics data analysis.
    Fisch KM; Meißner T; Gioia L; Ducom JC; Carland TM; Loguercio S; Su AI
    Bioinformatics; 2015 Jun; 31(11):1724-8. PubMed ID: 25637560
    [TBL] [Abstract][Full Text] [Related]  

  • 16. AIAP: A Quality Control and Integrative Analysis Package to Improve ATAC-seq Data Analysis.
    Liu S; Li D; Lyu C; Gontarz PM; Miao B; Madden PAF; Wang T; Zhang B
    Genomics Proteomics Bioinformatics; 2021 Aug; 19(4):641-651. PubMed ID: 34273560
    [TBL] [Abstract][Full Text] [Related]  

  • 17. MMGAT: a graph attention network framework for ATAC-seq motifs finding.
    Wu X; Hou W; Zhao Z; Huang L; Sheng N; Yang Q; Zhang S; Wang Y
    BMC Bioinformatics; 2024 Apr; 25(1):158. PubMed ID: 38643066
    [TBL] [Abstract][Full Text] [Related]  

  • 18. methylPipe and compEpiTools: a suite of R packages for the integrative analysis of epigenomics data.
    Kishore K; de Pretis S; Lister R; Morelli MJ; Bianchi V; Amati B; Ecker JR; Pelizzola M
    BMC Bioinformatics; 2015 Sep; 16():313. PubMed ID: 26415965
    [TBL] [Abstract][Full Text] [Related]  

  • 19. Association rule mining to identify transcription factor interactions in genomic regions.
    Ceddia G; Martino LN; Parodi A; Secchi P; Campaner S; Masseroli M
    Bioinformatics; 2020 Feb; 36(4):1007-1013. PubMed ID: 31504203
    [TBL] [Abstract][Full Text] [Related]  

  • 20. BayesPeak--an R package for analysing ChIP-seq data.
    Cairns J; Spyrou C; Stark R; Smith ML; Lynch AG; Tavaré S
    Bioinformatics; 2011 Mar; 27(5):713-4. PubMed ID: 21245054
    [TBL] [Abstract][Full Text] [Related]  

    [Next]    [New Search]
    of 11.