Man pages for alice-szeliga/keles-pipeline
A Model to Predict Regulatory and Expression Modulating eQTLs
| addAllToScoreList | Adds a score to the score list |
| addToScoreList | Adds a score to the score list |
| CheckEscoresCol | 'CheckEscoresCol' |
| construct_overlapping_encodepeaks | Calculates ENCODE chromatin scores |
| constructSummary8merScores | Summarizes results of 8mer scores |
| createAllCorrelations | Perform simple correlations |
| createEnrscoresList | Imports human and mouse data |
| CreateEscores | 'CreateEscores' is used to |
| create_fimo_predictors | Run all functions in here |
| createOutput | Create TF output |
| createSubseq21List | title |
| deepbindAnalysis | Exploratory analysis with Deepbind scores |
| dt2granges | Converts data.table to Granges |
| dt2uniquegranges | Converts data.table to UniqueGranges |
| encodeAnalysis | Exploratory analysis with ENCODE PWM scores |
| extract8mers | Extract all 8mers for given eQTL sequences |
| extract_encodepeaks | Extracts peaks from ENCODE data |
| factorBookAnalysis | Exploratory analysis with FactorBook PWM scores |
| getAllLists | Gets normal, unique, and narrowpeak bed files |
| getBedDF | Read in a bed file |
| getBedList | Turns bed files into data.tables |
| getBedNames | Get name of Bed files for all peaks |
| getCols3to5 | Returns 3rd to 5th columns |
| getCorrelation | 'getCorrelation' performs a simple correlation between a fimo... |
| getDefaultFileLocations | Get file locations of Data |
| getFactorName | Creates directory name for factor |
| getFastaName | Creates filename for FASTA file |
| getMetaPeaks | Combines all peak files from ENCODE |
| getRangeCols | Get range of a data.table's columns |
| GetSubseqCoordAbs | Get absolute coordinates for the subsequences |
| hello | Hello, World! |
| jasparAnalysis | Exploratory analysis with Jaspar PWM scores |
| loadFimoData | Load in FIMO summary data |
| makeScoreList | Creates a score list |
| outputAllScores | Output all scores |
| readChip | read in ChIP data from ENCODE |
| readDnameth | read in DNA methylation data from ENCODE |
| readDnase | read in Dnase data from ENCODE |
| removeHeader | Removes header from a data.table |
| run_encode | ENCODE data |
| runFimo | Run Fimo |
| run_fimo_and_summarize | Runs FactorBook, ENCODE and Jaspar on FIMO |
| run_Uniprobe_scores | Computing Uniprobe 8mer scores |
| saveOutput | Saves output to directory |
| simpleCap | Capitalizes words in a string |
| summarizeEncode | Summarize FIMO with ENCODE |
| summarizeFactorBook | Summarize FIMO with FactorBook |
| summarizeJaspar | Summarize FIMO with Jaspar |
