iRefR: iRefIndex Manager

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"iRefR" allows the user to load any version of the consolidated protein interaction database "iRefIndex" and perform tasks such as: selecting databases, pmids, experimental methods, searching for specific proteins, separate binary interactions from complexes and polymers, generate complexes according to an algorithm that looks after possible binary-represented complexes, make general database statistics and create network graphs, among others.

Author
Antonio Mora <antoniocmora@gmail.com>, Ian Donaldson <ian.oslo@gmail.com>
Date of publication
2013-12-17 19:35:08
Maintainer
Antonio Mora <antoniocmora@gmail.com>
License
GPL (>= 2)
Version
1.13
URLs

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Man pages

convert_complexList_to_MITAB
Convert complexList format to MITAB format
convert_edgeList_to_graph
Convert iRefIndex/edgeList table to Graph
convert_edgeList_to_MITAB
Convert edgeList format to MITAB format
convert_graph_to_edgeList
Convert Graph to iRefIndex/edgeList table
convert_MITAB_to_complexList
Convert MITAB format to complexList format
convert_MITAB_to_edgeList
Convert MITAB format to edgeList format
convert_protein_ID
Convert Protein Identifier
create_id_conversion_table
Create a Protein ID Conversion Table
get_irefindex
Get iRefIndex
merge_complexes_lists
Merge tables in complexList Format
select_confidence
Select the subset of iRefIndex corresponding to a set of...
select_database
Select iRefIndex Records belonging to given Primary...
select_interaction_type
Select Binary||Polymer||Complex in iRefIndex
select_protein
Get all iRefIndex records for a given Protein
summary_graph
Get Summary Information for a Graph
summary_protein
Get Summary Information for a given Protein
summary_table
Get Summary Information for a MITAB Table

Files in this package

iRefR
iRefR/inst
iRefR/inst/NEWS
iRefR/inst/doc
iRefR/inst/doc/iRefR_tutorial.pdf
iRefR/NAMESPACE
iRefR/R
iRefR/R/create_id_conversion_table.R
iRefR/R/convert_edgeList_to_graph.R
iRefR/R/merge_complexes_lists.R
iRefR/R/select_protein.R
iRefR/R/summary_table.R
iRefR/R/get_irefindex.R
iRefR/R/convert_graph_to_edgeList.R
iRefR/R/convert_edgeList_to_MITAB.R
iRefR/R/select_database.R
iRefR/R/summary_graph.R
iRefR/R/select_confidence.R
iRefR/R/select_interaction_type.R
iRefR/R/convert_MITAB_to_complexList.R
iRefR/R/convert_MITAB_to_edgeList.R
iRefR/R/convert_complexList_to_MITAB.R
iRefR/R/convert_protein_ID.R
iRefR/R/summary_protein.R
iRefR/MD5
iRefR/DESCRIPTION
iRefR/man
iRefR/man/summary_graph.Rd
iRefR/man/convert_graph_to_edgeList.Rd
iRefR/man/select_confidence.Rd
iRefR/man/convert_MITAB_to_edgeList.Rd
iRefR/man/summary_table.Rd
iRefR/man/merge_complexes_lists.Rd
iRefR/man/summary_protein.Rd
iRefR/man/convert_edgeList_to_graph.Rd
iRefR/man/select_protein.Rd
iRefR/man/select_database.Rd
iRefR/man/select_interaction_type.Rd
iRefR/man/convert_edgeList_to_MITAB.Rd
iRefR/man/create_id_conversion_table.Rd
iRefR/man/convert_complexList_to_MITAB.Rd
iRefR/man/get_irefindex.Rd
iRefR/man/convert_MITAB_to_complexList.Rd
iRefR/man/convert_protein_ID.Rd