Showing 12 of total 12 results (show query)
bioc
plotgardener:Coordinate-Based Genomic Visualization Package for R
Coordinate-based genomic visualization package for R. It grants users the ability to programmatically produce complex, multi-paneled figures. Tailored for genomics, plotgardener allows users to visualize large complex genomic datasets and provides exquisite control over how plots are placed and arranged on a page.
Maintained by Nicole Kramer. Last updated 5 months ago.
visualizationgenomeannotationfunctionalgenomicsgenomeassemblyhiccpp
309 stars 10.17 score 167 scripts 3 dependentsbioc
UCSC.utils:Low-level utilities to retrieve data from the UCSC Genome Browser
A set of low-level utilities to retrieve data from the UCSC Genome Browser. Most functions in the package access the data via the UCSC REST API but some of them query the UCSC MySQL server directly. Note that the primary purpose of the package is to support higher-level functionalities implemented in downstream packages like GenomeInfoDb or txdbmaker.
Maintained by Hervé Pagès. Last updated 2 months ago.
infrastructuregenomeassemblyannotationgenomeannotationdataimportbioconductor-packagecore-package
1 stars 10.09 score 4 scripts 1.7k dependentsbioc
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.
infrastructuredataimportannotationgenomeannotationgenomeassemblygeneticssequencingbioconductor-packagecore-package
3 stars 9.68 score 92 scripts 87 dependentsbioc
bambu:Context-Aware Transcript Quantification from Long Read RNA-Seq data
bambu is a R package for multi-sample transcript discovery and quantification using long read RNA-Seq data. You can use bambu after read alignment to obtain expression estimates for known and novel transcripts and genes. The output from bambu can directly be used for visualisation and downstream analysis such as differential gene expression or transcript usage.
Maintained by Ying Chen. Last updated 2 months ago.
alignmentcoveragedifferentialexpressionfeatureextractiongeneexpressiongenomeannotationgenomeassemblyimmunooncologylongreadmultiplecomparisonnormalizationrnaseqregressionsequencingsoftwaretranscriptiontranscriptomicsbambubioconductorlong-readsnanoporenanopore-sequencingrna-seqrna-seq-analysistranscript-quantificationtranscript-reconstructioncpp
203 stars 9.04 score 91 scripts 1 dependentsbioc
GenomicDistributions:GenomicDistributions: fast analysis of genomic intervals with Bioconductor
If you have a set of genomic ranges, this package can help you with visualization and comparison. It produces several kinds of plots, for example: Chromosome distribution plots, which visualize how your regions are distributed over chromosomes; feature distance distribution plots, which visualizes how your regions are distributed relative to a feature of interest, like Transcription Start Sites (TSSs); genomic partition plots, which visualize how your regions overlap given genomic features such as promoters, introns, exons, or intergenic regions. It also makes it easy to compare one set of ranges to another.
Maintained by Kristyna Kupkova. Last updated 5 months ago.
softwaregenomeannotationgenomeassemblydatarepresentationsequencingcoveragefunctionalgenomicsvisualization
26 stars 7.44 score 25 scriptsbioc
cogeqc:Systematic quality checks on comparative genomics analyses
cogeqc aims to facilitate systematic quality checks on standard comparative genomics analyses to help researchers detect issues and select the most suitable parameters for each data set. cogeqc can be used to asses: i. genome assembly and annotation quality with BUSCOs and comparisons of statistics with publicly available genomes on the NCBI; ii. orthogroup inference using a protein domain-based approach and; iii. synteny detection using synteny network properties. There are also data visualization functions to explore QC summary statistics.
Maintained by Fabrício Almeida-Silva. Last updated 5 months ago.
softwaregenomeassemblycomparativegenomicsfunctionalgenomicsphylogeneticsqualitycontrolnetworkcomparative-genomicsevolutionary-genomics
10 stars 6.08 score 20 scriptsbioc
circRNAprofiler:circRNAprofiler: An R-Based Computational Framework for the Downstream Analysis of Circular RNAs
R-based computational framework for a comprehensive in silico analysis of circRNAs. This computational framework allows to combine and analyze circRNAs previously detected by multiple publicly available annotation-based circRNA detection tools. It covers different aspects of circRNAs analysis from differential expression analysis, evolutionary conservation, biogenesis to functional analysis.
Maintained by Simona Aufiero. Last updated 5 months ago.
annotationstructuralpredictionfunctionalpredictiongenepredictiongenomeassemblydifferentialexpression
10 stars 5.78 score 5 scriptsbioc
easylift:An R package to perform genomic liftover
The easylift package provides a convenient tool for genomic liftover operations between different genome assemblies. It seamlessly works with Bioconductor's GRanges objects and chain files from the UCSC Genome Browser, allowing for straightforward handling of genomic ranges across various genome versions. One noteworthy feature of easylift is its integration with the BiocFileCache package. This integration automates the management and caching of chain files necessary for liftover operations. Users no longer need to manually specify chain file paths in their function calls, reducing the complexity of the liftover process.
Maintained by Abdullah Al Nahid. Last updated 5 months ago.
softwareworkflowstepsequencingcoveragegenomeassemblydataimport
5 stars 5.00 score 7 scriptsbioc
BSgenomeForge:Forge your own BSgenome data package
A set of tools to forge BSgenome data packages. Supersedes the old seed-based tools from the BSgenome software package. This package allows the user to create a BSgenome data package in one function call, simplifying the old seed-based process.
Maintained by Hervé Pagès. Last updated 5 months ago.
infrastructuredatarepresentationgenomeassemblyannotationgenomeannotationsequencingalignmentdataimportsequencematchingbioconductor-packagecore-package
4 stars 4.90 score 6 scriptsbioc
mobileRNA:mobileRNA: Investigate the RNA mobilome & population-scale changes
Genomic analysis can be utilised to identify differences between RNA populations in two conditions, both in production and abundance. This includes the identification of RNAs produced by multiple genomes within a biological system. For example, RNA produced by pathogens within a host or mobile RNAs in plant graft systems. The mobileRNA package provides methods to pre-process, analyse and visualise the sRNA and mRNA populations based on the premise of mapping reads to all genotypes at the same time.
Maintained by Katie Jeynes-Cupper. Last updated 5 months ago.
visualizationrnaseqsequencingsmallrnagenomeassemblyclusteringexperimentaldesignqualitycontrolworkflowstepalignmentpreprocessingbioinformaticsplant-science
3 stars 4.78 score 2 scriptsbioc
NoRCE:NoRCE: Noncoding RNA Sets Cis Annotation and Enrichment
While some non-coding RNAs (ncRNAs) are assigned critical regulatory roles, most remain functionally uncharacterized. This presents a challenge whenever an interesting set of ncRNAs needs to be analyzed in a functional context. Transcripts located close-by on the genome are often regulated together. This genomic proximity on the sequence can hint to a functional association. We present a tool, NoRCE, that performs cis enrichment analysis for a given set of ncRNAs. Enrichment is carried out using the functional annotations of the coding genes located proximal to the input ncRNAs. Other biologically relevant information such as topologically associating domain (TAD) boundaries, co-expression patterns, and miRNA target prediction information can be incorporated to conduct a richer enrichment analysis. To this end, NoRCE includes several relevant datasets as part of its data repository, including cell-line specific TAD boundaries, functional gene sets, and expression data for coding & ncRNAs specific to cancer. Additionally, the users can utilize custom data files in their investigation. Enrichment results can be retrieved in a tabular format or visualized in several different ways. NoRCE is currently available for the following species: human, mouse, rat, zebrafish, fruit fly, worm, and yeast.
Maintained by Gulden Olgun. Last updated 5 months ago.
biologicalquestiondifferentialexpressiongenomeannotationgenesetenrichmentgenetargetgenomeassemblygo
1 stars 4.60 score 6 scriptscran
geno2proteo:Finding the DNA and Protein Sequences of Any Genomic or Proteomic Loci
Using the DNA sequence and gene annotation files provided in 'ENSEMBL' <https://www.ensembl.org/index.html>, the functions implemented in the package try to find the DNA sequences and protein sequences of any given genomic loci, and to find the genomic coordinates and protein sequences of any given protein locations, which are the frequent tasks in the analysis of genomic and proteomic data.
Maintained by Yaoyong Li. Last updated 3 years ago.
geneticsproteomicssequencingannotationgenomeannotationgenomeassembly
2.00 score