
Package index
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install_dependencies()
- Install package dependencies
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searchApicoTFdb()
- Fetch data from ApicoTFdb
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searchGSC()
- Fetch articles for given gene IDs from Google Scholar
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searchHP()
- Fetch Protein-protein interaction for given gene IDs from Hit Predict database
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searchIpDb()
- Fetch orthologs from InParanoiDb
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searchKipho()
- Fetch Kinases and Phosphatases from Kipho Database
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searchMidb()
- Fetch Minor intron tables from MiDB
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searchMiip()
- Fetch Protein-Protein interactions from MIIP database
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searchMT()
- Fetch data tables from malaria.tools database
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searchPhPl()
- Fetch data tables from PhenoPlasm database
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searchPM()
- Fetch articles from PubMed database
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searchTedConsensus()
- Fetch protein domains from TED database
Fetching tables from databases
These functions helps users fetch annotations and data in form of tables from various databases.
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getEffLen()
- Get effective gene lengths form TPM calculation
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getMpmp()
- Quickly fetch data from MPMP database
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getPreconfiguredTable()
- Get pre-configured tables
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getTable()
- Get tables with custom fields
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listMCA()
- List data sets in MCA
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listVeupathdb()
- List genomes and metadata in VEuPathDB
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plotAllCondition()
- Making plots similar to malaria.tools
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plotDomain()
- Plotting domains on protein body
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plotStageSpecific()
- Making plots similar to malaria.tools
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easyAF2Signal()
- Check Signal peptide fidelity
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easyExpPlot()
- Plot Normalised expression quickly
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easyGOPlot()
- Quick ORA result plotting
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easyLabelTransfer()
- Easy label transfer from reference data
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easymakeOrgdb()
- Create Org.db package quickly
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easyMCA()
- Fetch data from Malaria Cell Atlas
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easyNOISeqAnnot()
- Get NOISeq::readData ready annotations
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easyPhplplottbl()
- Quickly plot PhenoPlasm summary tables
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easyPie()
- Pie chart to summarize searchMT results
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easytopGO()
- Performing quick ORA analysis
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easyTPM()
- Calculate TPM values from count data
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easyTxDbmaker()
- Quickly make TxDb object
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pdb2uniprot()
- Quick mapping of PDB IDs to Uiprot IDs
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toGeneid()
- Convert Other IDs to Ensembl gene IDs