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1,977 results

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Page 1
AnVILWorkflow: A runnable workflow package for Cloud-implemented bioinformatics analysis pipelines.
Oh S, Gravel-Pucillo K, Ramos M, Schatz MC, Davis S, Carey V, Morgan M, Waldron L. Oh S, et al. F1000Res. 2024 Oct 21;13:1257. doi: 10.12688/f1000research.155449.1. eCollection 2024. F1000Res. 2024. PMID: 39669685 Free PMC article.
This package is distributed through the Bioconductor project ( https://bioconductor.org/packages/AnVILWorkflow), and the source code is available through GitHub ( https://github.com/shbrief/AnVILWorkflow)....
This package is distributed through the Bioconductor project ( https://bioconductor.org/packages/AnVILWorkflow), and the sourc …
Molecular targets and mechanisms of Sijunzi decoction in the treatment of Parkinson's disease: evidence from network pharmacology, molecular docking, molecular dynamics simulation, and experimental validation.
Jiang Y, Wu W, Xie L, Zhou Y, Yang K, Wu D, Xu W, Fang R, Ge J. Jiang Y, et al. Front Pharmacol. 2024 Nov 26;15:1487474. doi: 10.3389/fphar.2024.1487474. eCollection 2024. Front Pharmacol. 2024. PMID: 39660000 Free PMC article.
The STRING platform was used to construct a protein-protein interaction (PPI) network. The Bioconductor database and RX64 (4.0.0) software were used to conduct Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis on the core target gene …
The STRING platform was used to construct a protein-protein interaction (PPI) network. The Bioconductor database and RX64 (4.0.0) sof …
demuxSNP: supervised demultiplexing single-cell RNA sequencing using cell hashing and SNPs.
Lynch MP, Wang Y, Ho Sui S, Gatto L, Culhane AC. Lynch MP, et al. Gigascience. 2024 Jan 2;13:giae090. doi: 10.1093/gigascience/giae090. Gigascience. 2024. PMID: 39607981 Free PMC article.
Data simulation and benchmarking pipelines as well as processed benchmarking data for 5-50% doublets are publicly available. demuxSNP is available as an R/Bioconductor package (https://doi.org/doi:10.18129/B9.bioc.demuxSNP)....
Data simulation and benchmarking pipelines as well as processed benchmarking data for 5-50% doublets are publicly available. demuxSNP is ava …
Role of the Egr2 Promoter Antisense RNA in Modulating the Schwann Cell Chromatin Landscape.
Martinez Moreno M, Karambizi D, Hwang H, Fregoso K, Michles MJ, Fajardo E, Fiser A, Tapinos N. Martinez Moreno M, et al. Biomedicines. 2024 Nov 13;12(11):2594. doi: 10.3390/biomedicines12112594. Biomedicines. 2024. PMID: 39595160 Free PMC article.
ChIP followed by DNA purification columns was used to perform qPCR for relevant promoters. Hi-C, HiC-DC+, R, Bioconductor, and TOBIAS were used for significant and differential loop analysis, identifications of COREs and CORE-promotor loops, comparisons of TF activity at p …
ChIP followed by DNA purification columns was used to perform qPCR for relevant promoters. Hi-C, HiC-DC+, R, Bioconductor, and TOBIAS …
A Systematic Identification of RNA-Binding Proteins (RBPs) Driving Aberrant Splicing in Cancer.
Lobato-Fernandez C, Gimeno M, San Martín A, Anorbe A, Rubio A, Ferrer-Bonsoms JA. Lobato-Fernandez C, et al. Biomedicines. 2024 Nov 13;12(11):2592. doi: 10.3390/biomedicines12112592. Biomedicines. 2024. PMID: 39595158 Free PMC article.
The new method provides more accurate predictions and is included in the Bioconductor package EventPointer 3.14. We tested the algorithm in four experiments involving knockdowns of seven different RBPs. ...
The new method provides more accurate predictions and is included in the Bioconductor package EventPointer 3.14. We tested the algori …
Lefser: Implementation of metagenomic biomarker discovery tool, LEfSe, in R.
Khleborodova A, Gamboa-Tuz SD, Ramos M, Segata N, Waldron L, Oh S. Khleborodova A, et al. Bioinformatics. 2024 Nov 25:btae707. doi: 10.1093/bioinformatics/btae707. Online ahead of print. Bioinformatics. 2024. PMID: 39585730
We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, with improvements to the original algorithm for performance, accuracy, and reproducibility. ...AVAILABILITY AND IMPLEMENTATION: Our software …
We present the lefser package to provide comparable functionality within the R/Bioconductor ecosystem of statistical analysis tools, …
PIPETS: a statistically informed, gene-annotation agnostic analysis method to study bacterial termination using 3'-end sequencing.
Furumo Q, Meyer MM. Furumo Q, et al. BMC Bioinformatics. 2024 Nov 23;25(1):363. doi: 10.1186/s12859-024-05982-5. BMC Bioinformatics. 2024. PMID: 39580611 Free PMC article.
RESULTS: We present PIPETS, (Poisson Identification of PEaks from Term-Seq data), an R package available on Bioconductor that provides a novel analysis method for 3'-end sequencing data. PIPETS is a statistically informed, gene-annotation agnostic methodology. ...
RESULTS: We present PIPETS, (Poisson Identification of PEaks from Term-Seq data), an R package available on Bioconductor that provide …
Addressing the mean-variance relationship in spatially resolved transcriptomics data with spoon.
Shah K, Guo B, Hicks SC. Shah K, et al. bioRxiv [Preprint]. 2024 Nov 8:2024.11.04.621867. doi: 10.1101/2024.11.04.621867. bioRxiv. 2024. PMID: 39574747 Free PMC article. Preprint.
A software implementation of our method is available at https://bioconductor.org/packages/spoon....
A software implementation of our method is available at https://bioconductor.org/packages/spoon....
Damsel: analysis and visualisation of DamID sequencing in R.
Page CG, Londsdale A, Mitchell KA, Schröder J, Harvey KF, Oshlack A. Page CG, et al. Bioinformatics. 2024 Nov 28;40(12):btae695. doi: 10.1093/bioinformatics/btae695. Bioinformatics. 2024. PMID: 39558607 Free PMC article.
SUMMARY: DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor package to provide an end to end analysis for DamID sequencing data within R. ...AVAILABILITY AND IMPLEMENTATION: The R package Damsel is ava …
SUMMARY: DamID sequencing is a technique to map the genome-wide interaction of a protein with DNA. Damsel is the first Bioconductor p …
CCAFE: Estimating Case and Control Allele Frequencies from GWAS Summary Statistics.
Stoneman HR, Price A, Gignoux CR, Hendricks AE. Stoneman HR, et al. bioRxiv [Preprint]. 2024 Oct 29:2024.10.24.619530. doi: 10.1101/2024.10.24.619530. bioRxiv. 2024. PMID: 39554201 Free PMC article. Preprint.
The R package CCAFE, with implementations of both methods, is freely available on Bioconductor and GitHub....
The R package CCAFE, with implementations of both methods, is freely available on Bioconductor and GitHub....
1,977 results

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