Package index • plasmoRUtils

Install dependencies

These functions provides CLI access to various databases

searchApicoTFdb(): Fetch data from ApicoTFdb
searchHP(): Fetch Protein-protein interaction for given gene IDs from Hit Predict database
searchIpDb(): Fetch orthologs from InParanoiDb
searchKipho(): Fetch Kinases and Phosphatases from Kipho Database
searchMidb(): Fetch Minor intron tables from MiDB
searchMiip(): Fetch Protein-Protein interactions from MIIP database
searchPhPl(): Fetch data tables from PhenoPlasm database
searchPM(): Fetch articles from PubMed database
searchRS(): Fetch articles from Research Square database
searchTedConsensus(): Fetch protein domains from TED database

These functions helps users fetch annotations and data in form of tables from various databases.

getEffLen(): Get effective gene lengths form TPM calculation
getMpmp(): Quickly fetch data from MPMP database
getpairedOrthologs(): Fetch paired orthologs
getPreconfiguredTable(): Get pre-configured tables
getPreconfiguredTableOrthomcl(): Get pre-configured tables from OrthoMCL-DB
getTable(): Get tables with custom fields
getTableAttributes(): Browse available VEuPathDB databases attributes
getTableVeupathdb(): Retrieve gene annotations using a mixed list of IDs
listipdb(): List species metadata present in InparanoiDB 9
listMCA(): List data sets in MCA
listOrthomcl(): List species metadata present in OrthoMCL
listVeupathdb(): List genomes and metadata in VEuPathDB

These functions helps users make publication ready plots quickly.

Perform ruting bioinfrmatic tasks on non-model organisms quick and easy.

easyAF2Signal(): Check Signal peptide fidelity
easyExpPlot(): Plot Normalised expression quickly
easyGOPlot(): Plot GO enrichment results
easyLabelTransfer(): Easy label transfer from reference data
easymakeOrgdb(): Quickly create an organism-specific OrgDb package
easyMCA(): Download data from the Malaria Cell Atlas
easyNOISeqAnnot(): Get NOISeq::readData ready annotations
easyPhplplottbl(): Quickly plot PhenoPlasm summary tables
easytopGO(): Performing quick ORA analysis using Fisher or KS and an explicit background
easyTPM(): Calculate transcripts per million (TPM) from counts
easyTxDbmaker(): Create a TxDb from VEuPathDB GFF3 annotations

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