Software for Computing and Annotating Genomic Ranges
Publication Date
August 08, 2013
Journal
PLOS Computational Biology
Authors
Michael Lawrence, Wolfgang Huber, Hervé Pagès, Patrick Aboyoun, et al
Volume
9
Issue
8
Pages
e1003118
DOI
http://doi.org/10.1371/journal.pcbi.1003118
Publisher URL
http://journals.plos.org/ploscompbiol/article?id=10.1371%2Fjournal.pcbi.1003118
PubMed
http://www.ncbi.nlm.nih.gov/pubmed/23950696
PubMed Central
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3738458
Europe PMC
http://europepmc.org/abstract/MED/23950696
Web of Science
000323885400001
Scopus
84883368195
Mendeley
http://www.mendeley.com/research/software-computing-annotating-genomic-ranges
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Figshare

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  • {"files"=>["https://ndownloader.figshare.com/files/1147231"], "description"=>"<p>Ranges for the first three reads in the ctcfReads object, storing the read alignments for the CTCF sample.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Functional genomics", "Genome analysis tools", "Genome expression analysis", "Genome sequencing", "Sequence analysis", "algorithms", "reads", "storing", "alignments", "ctcf"], "article_id"=>767694, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Michael Lawrence", "Wolfgang Huber", "Hervé Pagès", "Patrick Aboyoun", "Marc Carlson", "Robert Gentleman", "Martin T. Morgan", "Vincent J. Carey"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003118.t003", "stats"=>{"downloads"=>0, "page_views"=>6, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Ranges_for_the_first_three_reads_in_the_ctcfReads_object_storing_the_read_alignments_for_the_CTCF_sample_/767694", "title"=>"Ranges for the first three reads in the ctcfReads object, storing the read alignments for the CTCF sample.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 02:36:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147228"], "description"=>"<p>The GRanges instance includes location-specific information on 24 attributes of each call, including information on sequencer cycle, base call quality distribution, and other features of BAM-based variant calling as performed by GSNAP <a href=\"http://www.ploscompbiol.org/article/info:doi/10.1371/journal.pcbi.1003118#pcbi.1003118-Wu1\" target=\"_blank\">[11]</a>.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Functional genomics", "Genome analysis tools", "Genome expression analysis", "Genome sequencing", "Sequence analysis", "algorithms", "applied", "BAM", "encode", "ctcf", "ChIP-seq"], "article_id"=>767691, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Michael Lawrence", "Wolfgang Huber", "Hervé Pagès", "Patrick Aboyoun", "Marc Carlson", "Robert Gentleman", "Martin T. Morgan", "Vincent J. Carey"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003118.t004", "stats"=>{"downloads"=>1, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Partial_output_of_countVariants_applied_to_a_BAM_file_from_an_ENCODE_CTCF_ChIP_seq_experiment_/767691", "title"=>"Partial output of countVariants applied to a BAM file from an ENCODE CTCF ChIP-seq experiment.", "pos_in_sequence"=>0, "defined_type"=>3, "published_date"=>"2013-08-08 02:36:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147227"], "description"=>"<p>Top panels: distributions of alternate nucleotide proportions for on- and off-SNP allele-dependent CTCF binding events. Bottom panels: relationships between average call quality values and alternate nucleotide proportions are depicted using a 2D density estimate (darker regions correspond to higher density.).</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Functional genomics", "Genome analysis tools", "Genome expression analysis", "Genome sequencing", "Sequence analysis", "algorithms"], "article_id"=>767690, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Michael Lawrence", "Wolfgang Huber", "Hervé Pagès", "Patrick Aboyoun", "Marc Carlson", "Robert Gentleman", "Martin T. Morgan", "Vincent J. Carey"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003118.g006", "stats"=>{"downloads"=>0, "page_views"=>0, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Figure_6_/767690", "title"=>"Figure 6", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:36:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147221"], "description"=>"<p>The <i>any</i> mode detects hits with partial or complete overlap, while <i>within</i> requires that the query range represents a subregion of the subject range.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Functional genomics", "Genome analysis tools", "Genome expression analysis", "Genome sequencing", "Sequence analysis", "algorithms", "overlap", "adjacency"], "article_id"=>767684, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Michael Lawrence", "Wolfgang Huber", "Hervé Pagès", "Patrick Aboyoun", "Marc Carlson", "Robert Gentleman", "Martin T. Morgan", "Vincent J. Carey"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003118.g003", "stats"=>{"downloads"=>3, "page_views"=>9, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Illustration_of_overlap_top_and_adjacency_bottom_relationships_/767684", "title"=>"Illustration of overlap (top) and adjacency (bottom) relationships.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:36:11"}
  • {"files"=>["https://ndownloader.figshare.com/files/1147218"], "description"=>"<p>In the table, the columns <i>seqnames</i>, <i>start</i> and <i>end</i> locate the exons in the genome. The <i>strand</i> column indicates the direction of transcription. The exons are grouped into transcripts by <i>tx_id</i>, and the exon IDs are given by <i>exon_id</i>. Virtually all genomic data sets fit this pattern: genomic location, followed by a series of columns, often including strand and/or score, that annotate that location. In the plot, the rectangles represent exonic regions, and the arrows represent the introns, as well as the strand.</p>", "links"=>[], "tags"=>["Computational biology", "genomics", "Functional genomics", "Genome analysis tools", "Genome expression analysis", "Genome sequencing", "Sequence analysis", "algorithms", "exons", "derived", "ucsc"], "article_id"=>767681, "categories"=>["Information And Computing Sciences", "Biological Sciences"], "users"=>["Michael Lawrence", "Wolfgang Huber", "Hervé Pagès", "Patrick Aboyoun", "Marc Carlson", "Robert Gentleman", "Martin T. Morgan", "Vincent J. Carey"], "doi"=>"https://dx.doi.org/10.1371/journal.pcbi.1003118.g001", "stats"=>{"downloads"=>0, "page_views"=>7, "likes"=>0}, "figshare_url"=>"https://figshare.com/articles/_Tabular_top_and_visual_bottom_representation_of_the_exons_for_the_human_KRAS_gene_derived_from_the_UCSC_known_gene_annotation_/767681", "title"=>"Tabular (top) and visual (bottom) representation of the exons for the human <i>KRAS</i> gene, derived from the UCSC known gene annotation.", "pos_in_sequence"=>0, "defined_type"=>1, "published_date"=>"2013-08-08 02:36:11"}

PMC Usage Stats | Further Information

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Relative Metric

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