ArticleBMC bioinformatics2011
rnaSeqMap: a Bioconductor package for RNA sequencing data exploration.
Article in BMC bioinformatics, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 6 papers.
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
6 citing papers in PubMed.
- Article
- Article
- Differential expression analysis of RNA-seq data at single-base resolution.Biostatistics (Oxford, England) · 2014Article
- Identification of a p-coumarate degradation regulon in Rhodopseudomonas palustris by Xpression, an integrated tool for prokaryotic RNA-seq data processing.Applied and environmental microbiology · 2012Article
- Preferred analysis methods for single genomic regions in RNA sequencing revealed by processing the shape of coverage.Nucleic acids research · 2012Article
- Repetitive DNA and next-generation sequencing: computational challenges and solutions.Nature reviews. Genetics · 2011Review
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe throughput of commercially available sequencers has recently significantly increased. It has reached the point where measuring the RNA expression by the depth of coverage has become feasible even for largest genomes. The development of software tools is constantly following the progress of biological hardware. In particular, as RNA sequencing software can be regarded genome browsers, exon junction tools and statistical tools operating on counts of reads in predefined regions. The library rnaSeqMap, freely available via Bioconductor, is an RNA sequencing software which is independent of any biological hardware platform. It is based upon standard Bioconductor infrastructure for sequencing data and includes several novel features focused on deeper understanding of coverage expression profiles and discovery of novel transcription regions.
resultsrnaSeqMap is a toolbox for analyses that may be performed with the use of gene annotations or alternatively, in an unsupervised mode, on any genomic region to find novel or non-standard transcripts. The data back-end may be a MySQL database or a set of files in standard BAM format. The processing in R can be run on a machine without any particular hardware requirements, and scales linearly with the number of genomic loci and number of samples analyzed. The main features of rnaSeqMap include coverage operations, discovering irreducible regions of high expression, significance search and splicing analyses with nucleotide granularity.
conclusionsThis software may be used for a range of applications related to RNA sequencing by building customized analysis pipelines. The applicability and precision is expected to increase in parallel with the progress of the genome coverage in sequencers.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.