2019-1-2 · Codon Usage Analysis and Prediction of Gene Expressivity. R package for analysis and visualization of codon usage in DNA sequences. Main functionalities calculates different measures of CU bias and CU-based predictors of gene expressivity. performs gene set enrichment analysis for unannotated or KEGG/COG annotated DNA sequences.
During the prediction of novel acetylation and deacetylation sites in a KAT or HDAC specific way we used the ASEB method which employs a similar strategy as GSEA (Mootha et al. 2003 Subramanian et al. 2005 Guttman et al. 2009). We focused on finding sites similar in sequence with the discovered ones for each KAT or HDAC family including
PheLiM package (March 2016) PheLiM (Phenotypic Linear Model) integrates predictions of off- and on-target siRNA-induced down-regulation to infer gene-specific contributions to phenotypes that are measured in RNA interference screens.The inference of phenotype-critical genes from siRNA-based screens is challenging due to pervasive off-target effects of siRNAs.
2021-7-19 · Bioconductor version Release (3.13) Seq2pathway is a novel tool for functional gene-set (or termed as pathway) analysis of next-generation sequencing data consisting of "seq2gene" and "gene2path" components. The seq2gene links sequence-level measurements of genomic regions (including SNPs or point mutation coordinates) to gene-level scores and
2020-6-1 · a The PICRUSt2 method consists of phylogenetic placement hidden-state prediction and sample-wise gene and pathway abundance tabulation. ASV sequences and abundances are taken as input and gene
2021-5-27 · bioconductorcancer research. cancer research Clinical Cancer Research . bioconductor
2020-6-23 · Combinatorial and statistical prediction of gene expression from haplotype sequence B. Alpay P. Demetci Sorin Istrail and Derek Aguiar# Equal Contribution #Corresponding Author Bioinformatics (Oxford Press) vol.36 Supplement_1 p i194-i202. 2020
2007-3-7 · Abstract. Summary pcaMethods is a Bioconductor compliant library for computing principal component analysis (PCA) on incomplete data sets. The results can be analyzed directly or used to estimate missing values to enable the use of missing value sensitive statistical methods.
2019-1-2 · Codon Usage Analysis and Prediction of Gene Expressivity. R package for analysis and visualization of codon usage in DNA sequences. Main functionalities calculates different measures of CU bias and CU-based predictors of gene expressivity. performs gene set enrichment analysis for unannotated or KEGG/COG annotated DNA sequences.
2019-7-8 · The materials are located in the "R and Bioconductor" tab at the top right mainly. Links to slides are under the "slides" tab above. Finally there are some additional and miscellaneous materials in the "Misc." tab. Materials here are licensed as CC BY-NC-SA 4.0 Creative Commons License.
2020-11-8 · Collection of various measures and tools for lncRNA annotation prediction put inside a redistributable R package. The package contains two main algorithms lncRNA2GOA and TopoICSim. lncRNA2GOA tries to annotate novel genes (in this specific case lncRNAs) by using various correlation/geometric scoring methods on correlated expression data. After correlating/scoring the
2021-5-19 · 1.Select a gene expression dataset and a list of genes of interest. 2.Extract priors from the biomedical literature and public structured databases using the Predictive Networks web application. 3.Use the predictionet R package to infer a gene interaction network from priors and gene expression data. (a)Infer a network using the main function netinf.
2021-5-27 · bioconductorcancer research. cancer research Clinical Cancer Research . bioconductor
2015-5-15 · Abstract. Summary Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci adapted for advances in genome research.Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores.
project replacing the use of RNNs in gene-regulatory network prediction with ODEs. Python 1 0 0 0 Updated Jul 2 2021. gpuzoo Benchmarks of the gpuZoo implementations. systems-biology gpu-computing gene-regulatory-network This is a read-only mirror of the Bioconductor SVN repository.
Protein Subcellular Localization . LocDB is a expert curated database that collects experimental annotations for the subcellular localization of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana).The database also contains predictions of subcellular localization from a variety of state-of-the-art prediction methods for all proteins with experimental information.
2015-11-24 · Here we present the genefu R/Bioconductor package a multi-tiered compendium of bioinformatics algorithms and gene signatures for molecular subtyping and prognostication in breast cancer. Availability and implementation The genefu package is available from Bioconductor.
MiRcode provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation including >10 000 long non-coding RNA genes. Coding genes are also covered including atypical regions such as 5 UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan.
2012-8-22 · We have compared Affymetrix and Bioconductor annotations for the MOE430A (mouse) GeneChip® array. The mappings of probe sets to LocusLink identifiers (LocusIDs) were found to be dynamic with many changes between successive releases of annotation for both Affymetrix and Bioconductor. There are 49 probe sets that are assigned to one LocusID by Affymetrix and to a
2012-8-22 · We have compared Affymetrix and Bioconductor annotations for the MOE430A (mouse) GeneChip® array. The mappings of probe sets to LocusLink identifiers (LocusIDs) were found to be dynamic with many changes between successive releases of annotation for both Affymetrix and Bioconductor. There are 49 probe sets that are assigned to one LocusID by Affymetrix and to a
2 days ago · Bioconductor version Release (3.13) This package allows the use of multiple sources of co-data (e.g. external p-values gene lists annotation) to improve prediction of binary continuous and survival response using (logistic linear or Cox) group-regularized ridge regression. It also facilitates post-hoc variable selection and prediction
CelliD v0.99. R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. Welcome to the official Github repository of the CelliD software presented in the Article Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID Nature Biotechnology 2021. Overview
2016-1-21 · Abstract. Summary The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation.TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices.TFBStools provides a toolkit for handling TFBS profile matrices scanning
2015-5-15 · Abstract. Summary Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci adapted for advances in genome research.Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores.
CelliD v0.99. R package for gene signature extraction and cell identity recognition at individual cell level from single-cell RNA-seq. Welcome to the official Github repository of the CelliD software presented in the Article Gene signature extraction and cell identity recognition at the single-cell level with Cell-ID Nature Biotechnology 2021. Overview
2019-1-2 · Codon Usage Analysis and Prediction of Gene Expressivity. R package for analysis and visualization of codon usage in DNA sequences. Main functionalities calculates different measures of CU bias and CU-based predictors of gene expressivity. performs gene set enrichment analysis for unannotated or KEGG/COG annotated DNA sequences.
MiRcode provides "whole transcriptome" human microRNA target predictions based on the comprehensive GENCODE gene annotation including >10 000 long non-coding RNA genes. Coding genes are also covered including atypical regions such as 5 UTRs and CDS. MicroRNA family definitions and names are consistent with TargetScan.
2011-12-15 · gene list is provided in files/bild2006_ras_signature_348.csv and will serve as the core set of genes involved in the RAS pathway. 2.2 Colon cancer gene expression data We use two large gene expression datasets of primary colon tumors collected before any adjuvant therapy. The rst dataset provided in the predictionet package (see expOlon.ras) was
2012-11-3 · Bioconductor website -> Project -> Mailing lists Searchable Bioconductor mailing lists Functional genomics gene regulation network signaling pathway motif identification . Prediction Graphics . Useful R/BioC Packages Marray limma Spotted cDNA
2017-5-10 · 1. Introduction. Network Biology and Network Medicine opened new avenues for the discovery of the underlying biological and pathological properties of biological systems this context several prediction problems such as the automated prediction of protein functions (AFP) the drug-repositioning and gene prioritization problems and the prediction of gene-abnormal phenotypes
2021-3-1 · 2.6. Gene Set Enrichment Analysis (GSEA) GSEA is an analysis method for genome-wide expression profile chip data. It compares genes with a predefined gene set (usually from functional annotations or the results of previous experiments) and then checks whether the predefined gene set is in this ranking table enrichment at the top or bottom.
2015-5-15 · Abstract. Summary Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci adapted for advances in genome research.Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores.
2020-6-1 · a The PICRUSt2 method consists of phylogenetic placement hidden-state prediction and sample-wise gene and pathway abundance tabulation. ASV sequences and abundances are taken as input and gene
2021-5-27 · bioconductorcancer research. cancer research Clinical Cancer Research . bioconductor
Protein Subcellular Localization . LocDB is a expert curated database that collects experimental annotations for the subcellular localization of proteins in Human (Homo sapiens) and Weed (Arabidopsis thaliana).The database also contains predictions of subcellular localization from a variety of state-of-the-art prediction methods for all proteins with experimental information.
2015-11-24 · Notably using a single proliferation gene (AURKA) produces a similar performance to the majority of other predictors. 4 Application across data platforms. Many of the molecular subtyping algorithms and gene expression signatures implemented within genefu have originally been derived from microarray gene expression data. This raises an important question as to whether such methods can
project replacing the use of RNNs in gene-regulatory network prediction with ODEs. Python 1 0 0 0 Updated Jul 2 2021. gpuzoo Benchmarks of the gpuZoo implementations. systems-biology gpu-computing gene-regulatory-network This is a read-only mirror of the Bioconductor SVN repository.
2015-5-15 · Abstract. Summary Seq2pathway is an R/Python wrapper for pathway (or functional gene-set) analysis of genomic loci adapted for advances in genome research.Seq2pathway associates the biological significance of genomic loci with their target transcripts and then summarizes the quantified values on the gene-level into pathway scores.
2016-1-21 · Abstract. Summary The ability to efficiently investigate transcription factor binding sites (TFBSs) genome-wide is central to computational studies of gene regulation.TFBSTools is an R/Bioconductor package for the analysis and manipulation of TFBSs and their associated transcription factor profile matrices.TFBStools provides a toolkit for handling TFBS profile matrices scanning
2021-3-1 · 2.6. Gene Set Enrichment Analysis (GSEA) GSEA is an analysis method for genome-wide expression profile chip data. It compares genes with a predefined gene set (usually from functional annotations or the results of previous experiments) and then checks whether the predefined gene set is in this ranking table enrichment at the top or bottom.
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