R-universe search: genomicfeatures

Showing 6 of total 6 results (show query)

bioc

GenomicFeatures:Query the gene models of a given organism/assembly

Extract the genomic locations of genes, transcripts, exons, introns, and CDS, for the gene models stored in a TxDb object. A TxDb object is a small database that contains the gene models of a given organism/assembly. Bioconductor provides a small collection of TxDb objects in the form of ready-to-install TxDb packages for the most commonly studied organisms. Additionally, the user can easily make a TxDb object (or package) for the organism/assembly of their choice by using the tools from the txdbmaker package.

Maintained by H. Pagès. Last updated 4 months ago.

genetics infrastructure annotation sequencing genomeannotation bioconductor-package core-package

51.3 match 26 stars 15.34 score 5.3k scripts 339 dependents

huanglabumn

oncoPredict:Drug Response Modeling and Biomarker Discovery

Allows for building drug response models using screening data between bulk RNA-Seq and a drug response metric and two additional tools for biomarker discovery that have been developed by the Huang Laboratory at University of Minnesota. There are 3 main functions within this package. (1) calcPhenotype is used to build drug response models on RNA-Seq data and impute them on any other RNA-Seq dataset given to the model. (2) GLDS is used to calculate the general level of drug sensitivity, which can improve biomarker discovery. (3) IDWAS can take the results from calcPhenotype and link the imputed response back to available genomic (mutation and CNV alterations) to identify biomarkers. Each of these functions comes from a paper from the Huang research laboratory. Below gives the relevant paper for each function. calcPhenotype - Geeleher et al, Clinical drug response can be predicted using baseline gene expression levels and in vitro drug sensitivity in cell lines. GLDS - Geeleher et al, Cancer biomarker discovery is improved by accounting for variability in general levels of drug sensitivity in pre-clinical models. IDWAS - Geeleher et al, Discovering novel pharmacogenomic biomarkers by imputing drug response in cancer patients from large genomics studies.

Maintained by Robert Gruener. Last updated 12 months ago.

sva preprocesscore stringr biomart genefilter org.hs.eg.db genomicfeatures txdb.hsapiens.ucsc.hg19.knowngene tcgabiolinks biocgenerics genomicranges iranges s4vectors

10.0 match 18 stars 6.47 score 41 scripts

bioc

TCseq:Time course sequencing data analysis

Quantitative and differential analysis of epigenomic and transcriptomic time course sequencing data, clustering analysis and visualization of the temporal patterns of time course data.

Maintained by Mengjun Wu. Last updated 5 months ago.

epigenetics timecourse sequencing chipseq rnaseq differentialexpression clustering visualization

3.0 match 5.92 score 28 scripts 1 dependents

bioc

InPAS:Identify Novel Alternative PolyAdenylation Sites (PAS) from RNA-seq data

Alternative polyadenylation (APA) is one of the important post- transcriptional regulation mechanisms which occurs in most human genes. InPAS facilitates the discovery of novel APA sites and the differential usage of APA sites from RNA-Seq data. It leverages cleanUpdTSeq to fine tune identified APA sites by removing false sites.

Maintained by Jianhong Ou. Last updated 2 months ago.

alternative polyadenylation differential polyadenylation site usage rna-seq gene regulation transcription

1.7 match 4.30 score 1 scripts

bioc

ensembldb:Utilities to create and use Ensembl-based annotation databases

The package provides functions to create and use transcript centric annotation databases/packages. The annotation for the databases are directly fetched from Ensembl using their Perl API. The functionality and data is similar to that of the TxDb packages from the GenomicFeatures package, but, in addition to retrieve all gene/transcript models and annotations from the database, ensembldb provides a filter framework allowing to retrieve annotations for specific entries like genes encoded on a chromosome region or transcript models of lincRNA genes. EnsDb databases built with ensembldb contain also protein annotations and mappings between proteins and their encoding transcripts. Finally, ensembldb provides functions to map between genomic, transcript and protein coordinates.

Maintained by Johannes Rainer. Last updated 5 months ago.

genetics annotationdata sequencing coverage annotation bioconductor bioconductor-packages ensembl

0.5 match 35 stars 14.08 score 892 scripts 108 dependents

bioc

txdbmaker:Tools for making TxDb objects from genomic annotations

A set of tools for making TxDb objects from genomic annotations from various sources (e.g. UCSC, Ensembl, and GFF files). These tools allow the user to download the genomic locations of transcripts, exons, and CDS, for a given assembly, and to import them in a TxDb object. TxDb objects are implemented in the GenomicFeatures package, together with flexible methods for extracting the desired features in convenient formats.

Maintained by H. Pagès. Last updated 4 months ago.

infrastructure dataimport annotation genomeannotation genomeassembly genetics sequencing bioconductor-package core-package

0.5 match 3 stars 9.70 score 92 scripts 86 dependents