Man pages for vitkl/SLIMFinderR
Short Linear Motif Search Using QSLIMFinder, Protein Interaction Network and Binding Domain Inference
| benchmarkMotifs | Benchmark linear motif instance found using QSLIMFinder... |
| benchmarkMotifsROC | Plot ROC or precision-recall curves for motifs search... |
| centerDomains | Center QSLIMFinder datasets (InteractionSubsetFASTA_list) at... |
| domainProteinPairMatch | Check if the protein in the set2 is associated with domain... |
| ELMdb2GRanges | Download and read ELM database motif occurrences |
| filterBYmotifType | Filter ELM database motif occurrence GRanges by motif type |
| filterInteractionSubsetFASTA_list | Filter InteractionSubsetFASTA_list by the size of the... |
| findOverlapsBench | Find occuring GRanges overlapping with the benchmarking set... |
| GRangesINinteractionSubsetFASTA | Check if proteins in GRanges were used for motif search using... |
| interactionSubsetFASTA | FASTA sequences of interactors of a specific protein |
| interactionSubsetMapID | interaction_subset_from_2_sets renames ids in the... |
| listInteractionSubsetFASTA | get FASTA sequences of proteins that interact with seed... |
| listSingleInteractFromSet2 | Split interaction subset from 2 sets so that each elements... |
| merge2GRangesmcols | Merge data.table to GRanges metadata |
| motifVariantClass | Generate motif variant class (the first 2 element in the... |
| plotEnrichment | Plot the enrichment of domains that are likely to be... |
| PPInetwork2SLIMFinder | Find linear motifs (QSLIMFinder or SLIMFinder) in the protein... |
| printMotifDomainTable | 'printMotifDomainTable' combines Domain enrichment and Motif... |
| QSLIMFinderCommand | Generate a QSLIMFinder command |
| randomGRanges | Generate random GRanges of equal length in the same sequence |
| readQSLIMFinderMain | Read and write QSLIMFinder results |
| recodeANDinteractionSubsetFASTA | Recode names and retrieve FASTA sequences of interactors of a... |
| recodeFASTA | Recode names of the AAStringSet object |
| reduceOverlappingGRanges | Reduce Overlapping GRanges keeping metadata (collapsing... |
| reduceWithMcols | Reduce GRanges keeping metadata (collapsing withing each... |
| runCompariMotif3 | Run CompariMotif3 |
| runQSLIMFinder | Run a list of QSLIMFinder jobs |
| singleInteractFromSet2 | Filter interaction subset from 2 sets: keep only i-th element... |
| SLIMFinderOcc2GRanges | Read QSLIMFinder (SLIMFinder) occurence output to Genomic... |
| subset2setsBy1ID | Subset 2 sets of protein interaction data using a single ID... |
| writeInteractionSubsetFASTA_list | Write InteractionSubsetFASTA_list into directory system... |
