Files in alice-szeliga/keles-pipeline

A Model to Predict Regulatory and Expression Modulating eQTLs

R/base_getDefaultFileLocations.R R/base_runAll.R R/deepbind_run_Deepbind.R R/encode_DFToGranges.R R/encode_construct_overlapping.encodepeaks.narrow1_SS.R R/encode_extract_encodepeaks.R R/encode_run_Encode.R R/fimo_create_fimo_predictors.R R/fimo_run_Fimo.R R/fimo_run_fimo_and_summarize.R R/originalCode/8merScores.R R/originalCode/construct_summary.8merscores_ref_SS.v2.R R/originalCode/create_fimo_predictors_alt.R R/originalCode/create_fimo_predictors_ref.R R/originalCode/extract_8merscores_ref_SS.v2.R R/originalCode/run_fimo_and_summarize_alt.R R/originalCode/run_fimo_and_summarize_ref.R R/sandbox/extract_8merscores_ref_SS_MODIFIED.v2.R R/sandbox/pipeline_draft1.R R/sandbox/pipeline_draft2.R R/sandbox/sandbox1.R R/uniprobe_8merScores.R R/uniprobe_construct_summary.8merscores_ref_SS.R R/uniprobe_extract_8merscores_ref_SS.R R/uniprobe_run_Uniprobe.R README.md man/CheckEscoresCol.Rd man/CreateEscores.Rd man/GetSubseqCoordAbs.Rd man/addAllToScoreList.Rd man/addToScoreList.Rd man/constructSummary8merScores.Rd man/construct_overlapping_encodepeaks.Rd man/createAllCorrelations.Rd man/createEnrscoresList.Rd man/createOutput.Rd man/createSubseq21List.Rd man/create_fimo_predictors.Rd man/deepbindAnalysis.Rd man/dt2granges.Rd man/dt2uniquegranges.Rd man/encodeAnalysis.Rd man/extract8mers.Rd man/extract_encodepeaks.Rd man/factorBookAnalysis.Rd man/getAllLists.Rd man/getBedDF.Rd man/getBedList.Rd man/getBedNames.Rd man/getCols3to5.Rd man/getCorrelation.Rd man/getDefaultFileLocations.Rd man/getFactorName.Rd man/getFastaName.Rd man/getMetaPeaks.Rd man/getRangeCols.Rd man/hello.Rd man/jasparAnalysis.Rd man/loadFimoData.Rd man/makeScoreList.Rd man/outputAllScores.Rd man/readChip.Rd man/readDnameth.Rd man/readDnase.Rd man/removeHeader.Rd man/runFimo.Rd man/run_Uniprobe_scores.Rd man/run_encode.Rd man/run_fimo_and_summarize.Rd man/saveOutput.Rd man/simpleCap.Rd man/summarizeEncode.Rd man/summarizeFactorBook.Rd man/summarizeJaspar.Rd tests/testthat.R tests/testthat/test_8merscores.R tests/testthat/test_construct_overlapping.encodepeaks.R tests/testthat/test_construct_summary8merscores.R tests/testthat/test_extract_8merscores.R tests/testthat/test_extract_encodepeaks.R tests/testthat/test_fimo_create_fimo_predictors.R tests/testthat/test_fimo_run_fimo_and_summarize.R