Package index • plasmoRUtils

Install dependencies

install_dependencies(): Install package dependencies

Search functions

These functions provides CLI access to various databases

searchApicoTFdb(): Fetch data from ApicoTFdb

searchGSC(): Fetch articles for given gene IDs from Google Scholar

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

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.

getEffLen(): Get effective gene lengths form TPM calculation

getMpmp(): Quickly fetch data from MPMP database

getpairedOrthologs(): Fetch paired orthologs

getPreconfiguredTable(): Get pre-configured tables

getTable(): Get tables with custom fields

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

Plotting functions

These functions helps users make publication ready plots quickly.

plotAllCondition(): Making plots similar to malaria.tools

plotDomain(): Plotting domains on protein body

plotStageSpecific(): Making plots similar to malaria.tools

Easy functions

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

easyAF2Signal(): Check Signal peptide fidelity

easyExpPlot(): Plot Normalised expression quickly

easyGOPlot(): Quick ORA result plotting

easyLabelTransfer(): Easy label transfer from reference data

easymakeOrgdb(): Create Org.db package quickly

easyMCA(): Fetch data from Malaria Cell Atlas

easyNOISeqAnnot(): Get NOISeq::readData ready annotations

easyPhplplottbl(): Quickly plot PhenoPlasm summary tables

easytopGO(): Performing quick ORA analysis

easyTPM(): Calculate TPM values from count data

easyTxDbmaker(): Quickly make TxDb object

ID conversin

Convert one ID type to another

pdb2uniprot(): Quick mapping of PDB IDs to Uiprot IDs

toGeneid(): Convert Other IDs to Ensembl gene IDs