Skip to contents

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
searchMT()
Fetch data tables from malaria.tools 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
getPreconfiguredTable()
Get pre-configured tables
getTable()
Get tables with custom fields
listMCA()
List data sets in MCA
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
easyPie()
Pie chart to summarize searchMT results
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