Wolfram Function Repository

Instant-use add-on functions for the Wolfram Language

Function Repository Resource:

 UCSCGenomeTrackData

Source Notebook

Retrieve genome track data accessible in the UCSC Genome Browser database

Contributed by: Keiko Hirayama

ResourceFunction["UCSCGenomeTrackData"]["Hubs"]

gives the dataset of available public hubs to access assembled genomics information.

ResourceFunction["UCSCGenomeTrackData"]["hub","genome"]

gives the dataset of available genome tracks from a specified hub and genome.

ResourceFunction["UCSCGenomeTrackData"]["hub","genome","track"]

gives the track dataset for a specified track from a specified hub and genome.

ResourceFunction["UCSCGenomeTrackData"]["hub","genome","track","chromosome"]

gives the track dataset for a specified track and chromosome from a specified hub and genome.

ResourceFunction["UCSCGenomeTrackData"]["hub","genome","track","chromosome",{start,end}]

gives the track dataset for a specified track and chromosome from a specified huband genome. Coordinates of the chromosome are given by the start and end positions.

ResourceFunction["UCSCGenomeTrackData"]["hub","genome","track",MetaInformation]

gives the metainformation on available track properties for a specified track from a specified hub and genome.

Details

Genome track data is based on the public hubs accessible in the UCSC Genome Browser database [1].

Examples

Basic Examples (3) 

Retrieve the list of public hubs to access genomics information:

In[1]:=
ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["Hubs"]
Out[1]=

Retrieve the dataset of available genome tracks from the latest human assemblies in the UCSC Genome Browser database:

In[2]:=
ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["UCSC Genome Browser", "hg38"]
Out[2]=

Retrieve the known genes in the human X chromosome:

In[3]:=
ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["UCSC Genome Browser", "hg38", "knownGene", "X"]
Out[3]=

Scope (2) 

Retrieve pathogenicity information for the specified regions of human chromosome 1:

In[4]:=
ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["dbVar Hub", "hg38", "clinvar_pathogenic", "1", {1000000, 1001000}]
Out[4]=

Retrieve meta information on properties accessible for a specified genome track:

In[5]:=
ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["ABC of cellular microRNAome", "hg38", "primary_cells", MetaInformation]
Out[5]=

Applications (3) 

Access LIBD Human DLPFC Development hub and retrieve data from the differential expression analysis of the developing human brain:

In[6]:=
ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["LIBD Human DLPFC Development", "hg19"]
Out[6]=

Find F-statistics for differential expression regions across six age groups for the chromosome Y:

In[7]:=
fval = ResourceFunction[ "UCSCGenomeTrackData", ResourceSystemBase -> "https://www.wolframcloud.com/obj/resourcesystem/api/1.0"]["LIBD Human DLPFC Development", "hg19", "sixGroup_F", "Y"]
Out[7]=

Plot the F-values across the length of the chromosome:

In[8]:=
ListLinePlot[ Flatten[Normal@fval[All, {{#start, #value}, {#end, #value}} &], 1], Sequence[ Filling -> Axis, AxesLabel -> {"chromosome position", "F-value"}]]
Out[8]=

Requirements

Wolfram Language 13.0 (December 2021) or above

Version History

  • 1.0.0 – 12 April 2024

Source Metadata

  • Citation:
    • [1] Raney BJ, Barber GP, Benet-Pagès A, Casper J, Clawson H, Cline MS, Diekhans M, Fischer C, Navarro Gonzalez J, Hickey G et al. The UCSC Genome Browser database: 2024 update. Nucleic Acids Res. 2024 Jan 5;52(D1):D1082-D1088. PMID: 37953330; PMC: PMC10767968

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