Files in jianhong/enhancerHomologSearch

Identification of putative mammalian orthologs to given enhancer

.Rbuildignore

.gitignore

DESCRIPTION

NAMESPACE

NEWS

R/RcppExports.R R/alignment.R R/conservedMotifs.R R/enhancers.R R/getENCODEdata.R R/motifs.R R/queryEncode.R R/saveAlignments.R R/searchTFBPS.R R/shuffle.R R/utils.R README.md

data/motifs.rda

inst/extdata/al.rds

inst/extdata/aln_hs.rds

inst/extdata/aln_mm.rds

inst/extdata/motifs.R inst/extdata/tmpdata.R man/Enhancers-class.Rd man/alignment.Rd man/alignmentOne.Rd man/conservedMotifs.Rd man/getENCODEdata.Rd man/motifs.Rd man/queryEncode.Rd man/saveAlignments.Rd man/searchTFBPS.Rd man/shuffle.Rd

src/ClustalW/Clustal.cpp

src/ClustalW/Clustal.h

src/ClustalW/Help.cpp

src/ClustalW/Help.h

src/ClustalW/alignment/Alignment.cpp

src/ClustalW/alignment/Alignment.h

src/ClustalW/alignment/AlignmentOutput.cpp

src/ClustalW/alignment/AlignmentOutput.h

src/ClustalW/alignment/ObjectiveScore.cpp

src/ClustalW/alignment/ObjectiveScore.h

src/ClustalW/alignment/Sequence.cpp

src/ClustalW/alignment/Sequence.h

src/ClustalW/clustalw_version.h

src/ClustalW/fileInput/ClustalFileParser.cpp

src/ClustalW/fileInput/ClustalFileParser.h

src/ClustalW/fileInput/EMBLFileParser.cpp

src/ClustalW/fileInput/EMBLFileParser.h

src/ClustalW/fileInput/FileParser.cpp

src/ClustalW/fileInput/FileParser.h

src/ClustalW/fileInput/FileReader.cpp

src/ClustalW/fileInput/FileReader.h

src/ClustalW/fileInput/GDEFileParser.cpp

src/ClustalW/fileInput/GDEFileParser.h

src/ClustalW/fileInput/InFileStream.cpp

src/ClustalW/fileInput/InFileStream.h

src/ClustalW/fileInput/MSFFileParser.cpp

src/ClustalW/fileInput/MSFFileParser.h

src/ClustalW/fileInput/PIRFileParser.cpp

src/ClustalW/fileInput/PIRFileParser.h

src/ClustalW/fileInput/PearsonFileParser.cpp

src/ClustalW/fileInput/PearsonFileParser.h

src/ClustalW/fileInput/RSFFileParser.cpp

src/ClustalW/fileInput/RSFFileParser.h

src/ClustalW/general/Array2D.h

src/ClustalW/general/ClustalWResources.cpp

src/ClustalW/general/ClustalWResources.h

src/ClustalW/general/DebugLog.cpp

src/ClustalW/general/DebugLog.h

src/ClustalW/general/InvalidCombination.cpp

src/ClustalW/general/OutputFile.cpp

src/ClustalW/general/OutputFile.h

src/ClustalW/general/RandomAccessLList.h

src/ClustalW/general/SequenceNotFoundException.h

src/ClustalW/general/SquareMat.h

src/ClustalW/general/Stats.cpp

src/ClustalW/general/Stats.h

src/ClustalW/general/SymMatrix.cpp

src/ClustalW/general/SymMatrix.h

src/ClustalW/general/UserParameters.cpp

src/ClustalW/general/UserParameters.h

src/ClustalW/general/Utility.cpp

src/ClustalW/general/Utility.h

src/ClustalW/general/VectorOutOfRange.cpp

src/ClustalW/general/VectorOutOfRange.h

src/ClustalW/general/VectorUtility.h

src/ClustalW/general/clustalw.h

src/ClustalW/general/debuglogObject.h

src/ClustalW/general/general.h

src/ClustalW/general/param.h

src/ClustalW/general/statsObject.h

src/ClustalW/general/userparams.h

src/ClustalW/general/utils.h

src/ClustalW/interface/CommandLineParser.cpp

src/ClustalW/interface/CommandLineParser.h

src/ClustalW/multipleAlign/Iteration.cpp

src/ClustalW/multipleAlign/Iteration.h

src/ClustalW/multipleAlign/LowScoreSegProfile.cpp

src/ClustalW/multipleAlign/LowScoreSegProfile.h

src/ClustalW/multipleAlign/MSA.cpp

src/ClustalW/multipleAlign/MSA.h

src/ClustalW/multipleAlign/MyersMillerProfileAlign.cpp

src/ClustalW/multipleAlign/MyersMillerProfileAlign.h

src/ClustalW/multipleAlign/ProfileAlignAlgorithm.h

src/ClustalW/multipleAlign/ProfileBase.cpp

src/ClustalW/multipleAlign/ProfileBase.h

src/ClustalW/multipleAlign/ProfileStandard.cpp

src/ClustalW/multipleAlign/ProfileStandard.h

src/ClustalW/multipleAlign/ProfileWithSub.cpp

src/ClustalW/multipleAlign/ProfileWithSub.h

src/ClustalW/pairwise/FastPairwiseAlign.cpp

src/ClustalW/pairwise/FastPairwiseAlign.h

src/ClustalW/pairwise/FullPairwiseAlign.cpp

src/ClustalW/pairwise/FullPairwiseAlign.h

src/ClustalW/pairwise/PairwiseAlignBase.h

src/ClustalW/substitutionMatrix/SubMatrix.cpp

src/ClustalW/substitutionMatrix/SubMatrix.h

src/ClustalW/substitutionMatrix/globalmatrix.h

src/ClustalW/substitutionMatrix/matrices.h

src/ClustalW/tree/AlignmentSteps.cpp

src/ClustalW/tree/AlignmentSteps.h

src/ClustalW/tree/ClusterTree.cpp

src/ClustalW/tree/ClusterTree.h

src/ClustalW/tree/ClusterTreeAlgorithm.h

src/ClustalW/tree/ClusterTreeOutput.cpp

src/ClustalW/tree/ClusterTreeOutput.h

src/ClustalW/tree/NJTree.cpp

src/ClustalW/tree/NJTree.h

src/ClustalW/tree/RandomGenerator.cpp

src/ClustalW/tree/RandomGenerator.h

src/ClustalW/tree/Tree.cpp

src/ClustalW/tree/Tree.h

src/ClustalW/tree/TreeInterface.cpp

src/ClustalW/tree/TreeInterface.h

src/ClustalW/tree/UPGMA/Node.cpp

src/ClustalW/tree/UPGMA/Node.h

src/ClustalW/tree/UPGMA/RootedClusterTree.cpp

src/ClustalW/tree/UPGMA/RootedClusterTree.h

src/ClustalW/tree/UPGMA/RootedGuideTree.cpp

src/ClustalW/tree/UPGMA/RootedGuideTree.h

src/ClustalW/tree/UPGMA/RootedTreeOutput.cpp

src/ClustalW/tree/UPGMA/RootedTreeOutput.h

src/ClustalW/tree/UPGMA/UPGMAAlgorithm.cpp

src/ClustalW/tree/UPGMA/UPGMAAlgorithm.h

src/ClustalW/tree/UPGMA/upgmadata.h

src/ClustalW/tree/UnRootedClusterTree.cpp

src/ClustalW/tree/UnRootedClusterTree.h

src/ClustalW/tree/dayhoff.h

src/Makevars

src/Makevars.win

src/Muscle/README.txt

src/Muscle/aligngivenpath.cpp

src/Muscle/aligngivenpathsw.cpp

src/Muscle/aligntwomsas.cpp

src/Muscle/aligntwoprofs.cpp

src/Muscle/aln.cpp

src/Muscle/alpha.cpp

src/Muscle/alpha.h

src/Muscle/anchors.cpp

src/Muscle/bittraceback.cpp

src/Muscle/blosum62.cpp

src/Muscle/blosumla.cpp

src/Muscle/clust.cpp

src/Muscle/clust.h

src/Muscle/cluster.cpp

src/Muscle/cluster.h

src/Muscle/clustset.h

src/Muscle/clustsetdf.h

src/Muscle/clustsetmsa.h

src/Muscle/clwwt.cpp

src/Muscle/color.cpp

src/Muscle/cons.cpp

src/Muscle/diaglist.cpp

src/Muscle/diaglist.h

src/Muscle/diffobjscore.cpp

src/Muscle/diffpaths.cpp

src/Muscle/difftrees.cpp

src/Muscle/difftreese.cpp

src/Muscle/distcalc.cpp

src/Muscle/distcalc.h

src/Muscle/distfunc.cpp

src/Muscle/distfunc.h

src/Muscle/distpwkimura.cpp

src/Muscle/domuscle.cpp

src/Muscle/dosp.cpp

src/Muscle/dpregionlist.h

src/Muscle/dpreglist.cpp

src/Muscle/dpreglist.h

src/Muscle/drawtree.cpp

src/Muscle/edgelist.cpp

src/Muscle/edgelist.h

src/Muscle/enumopts.cpp

src/Muscle/enumopts.h

src/Muscle/enums.h

src/Muscle/enumtostr.cpp

src/Muscle/estring.cpp

src/Muscle/estring.h

src/Muscle/fasta.cpp

src/Muscle/fasta2.cpp

src/Muscle/fastclust.cpp

src/Muscle/fastdist.cpp

src/Muscle/fastdistjones.cpp

src/Muscle/fastdistkbit.cpp

src/Muscle/fastdistkmer.cpp

src/Muscle/fastdistmafft.cpp

src/Muscle/fastdistnuc.cpp

src/Muscle/fastscorepath2.cpp

src/Muscle/finddiags.cpp

src/Muscle/finddiagsn.cpp

src/Muscle/gapscoredimer.h

src/Muscle/glbalign.cpp

src/Muscle/glbalign352.cpp

src/Muscle/glbaligndiag.cpp

src/Muscle/glbalignla.cpp

src/Muscle/glbalignle.cpp

src/Muscle/glbalignns.cpp

src/Muscle/glbalignsimple.cpp

src/Muscle/glbalignsp.cpp

src/Muscle/glbalignspn.cpp

src/Muscle/glbalignss.cpp

src/Muscle/glbalndimer.cpp

src/Muscle/globals.cpp

src/Muscle/globalslinux.cpp

src/Muscle/globalsosx.cpp

src/Muscle/globalsother.cpp

src/Muscle/globalswin32.cpp

src/Muscle/gonnet.cpp

src/Muscle/gonnet.h

src/Muscle/gotowt.cpp

src/Muscle/henikoffweight.cpp

src/Muscle/henikoffweightpb.cpp

src/Muscle/html.cpp

src/Muscle/hydro.cpp

src/Muscle/intmath.cpp

src/Muscle/intmath.h

src/Muscle/local.cpp

src/Muscle/main.cpp

src/Muscle/make.err

src/Muscle/make.out

src/Muscle/makerootmsa.cpp

src/Muscle/makerootmsab.cpp

src/Muscle/maketree.cpp

src/Muscle/mhack.cpp

src/Muscle/mk

src/Muscle/mpam200.cpp

src/Muscle/msa.cpp

src/Muscle/msa.h

src/Muscle/msa2.cpp

src/Muscle/msadist.h

src/Muscle/msadistkimura.cpp

src/Muscle/msadistkimura.h

src/Muscle/msadistmafft.h

src/Muscle/msf.cpp

src/Muscle/muscle.cpp

src/Muscle/muscle.h

src/Muscle/muscleout.cpp

src/Muscle/nucmx.cpp

src/Muscle/nwdasimple.cpp

src/Muscle/nwdasimple2.cpp

src/Muscle/nwdasmall.cpp

src/Muscle/nwrec.cpp

src/Muscle/nwsmall.cpp

src/Muscle/objscore.cpp

src/Muscle/objscore.h

src/Muscle/objscore2.cpp

src/Muscle/objscoreda.cpp

src/Muscle/onexception.cpp

src/Muscle/options.cpp

src/Muscle/outweights.cpp

src/Muscle/pam200mafft.cpp

src/Muscle/params.cpp

src/Muscle/params.h

src/Muscle/phy.cpp

src/Muscle/phy2.cpp

src/Muscle/phy3.cpp

src/Muscle/phy4.cpp

src/Muscle/phyfromclust.cpp

src/Muscle/phyfromfile.cpp

src/Muscle/physeq.cpp

src/Muscle/phytofile.cpp

src/Muscle/posgap.cpp

src/Muscle/ppscore.cpp

src/Muscle/profdb.cpp

src/Muscle/profile.cpp

src/Muscle/profile.h

src/Muscle/profilefrommsa.cpp

src/Muscle/progalign.cpp

src/Muscle/progress.cpp

src/Muscle/progressivealign.cpp

src/Muscle/pwpath.cpp

src/Muscle/pwpath.h

src/Muscle/readmx.cpp

src/Muscle/realigndiffs.cpp

src/Muscle/realigndiffse.cpp

src/Muscle/refine.cpp

src/Muscle/refinehoriz.cpp

src/Muscle/refinesubfams.cpp

src/Muscle/refinetree.cpp

src/Muscle/refinetreee.cpp

src/Muscle/refinevert.cpp

src/Muscle/refinew.cpp

src/Muscle/releases.txt

src/Muscle/savebest.cpp

src/Muscle/scoredist.cpp

src/Muscle/scoregaps.cpp

src/Muscle/scorehistory.cpp

src/Muscle/scorehistory.h

src/Muscle/scorepp.cpp

src/Muscle/seq.cpp

src/Muscle/seq.h

src/Muscle/seqvect.cpp

src/Muscle/seqvect.h

src/Muscle/setblosumweights.cpp

src/Muscle/setgscweights.cpp

src/Muscle/setnewhandler.cpp

src/Muscle/spfast.cpp

src/Muscle/sptest.cpp

src/Muscle/stabilize.cpp

src/Muscle/subfam.cpp

src/Muscle/subfams.cpp

src/Muscle/svnmods.h

src/Muscle/svnversion.h

src/Muscle/sw.cpp

src/Muscle/termgaps.cpp

src/Muscle/textfile.cpp

src/Muscle/textfile.h

src/Muscle/threewaywt.cpp

src/Muscle/timing.h

src/Muscle/tomhydro.cpp

src/Muscle/traceback.cpp

src/Muscle/tracebackopt.cpp

src/Muscle/tracebacksw.cpp

src/Muscle/tree.h

src/Muscle/treefrommsa.cpp

src/Muscle/types.h

src/Muscle/typetostr.cpp

src/Muscle/unixio.h

src/Muscle/upgma2.cpp

src/Muscle/usage.cpp

src/Muscle/validateids.cpp

src/Muscle/version.txt

src/Muscle/vtml2.cpp

src/Muscle/writescorefile.cpp

src/RClustalW.cpp

src/RClustalW.h

src/RClustalWMain.cpp

src/RClustalWMain.h

src/RMuscle.cpp

src/RMuscle.h

src/RcppExports.cpp

src/ushuffle.c

src/ushuffle.h

src/ushuffler.cpp

tests/runTests.R tests/testthat/test_Enhancer_getSeq.R tests/testthat/test_alignmentOne.R tests/testthat/test_guessAssembly.R tests/testthat/test_searchTFBPS.R

vignettes/bibliography.bib

vignettes/enhancerHomologSearch.Rmd

vignettes/nature.csl

jianhong/enhancerHomologSearch documentation built on March 25, 2024, 10:06 a.m.