API for frenkiboy/MyLib

Global functions
AnnotateRegionPWM Source code
AnnotateRegions Source code
Annotate_Bamfiles Source code
Annotate_Divergent_Convergent Source code
Annotate_Peaks Source code
Annotate_Reads Source code
Assigner Source code
BEDCoverageToDataFrame Source code
BamIndex Source code
BamName Source code
BamReader Source code
BamReaderChr Source code
BamSelectBed Source code
BamSort Source code
BamToBedGraph Source code
BamToGRanges Source code
BamWindowerChr Source code
BedToGRanges Source code
BigFeatureOverlapBED Source code
BigFeatureOverlapBED.para Source code
BigPeakSplitter Source code
BigToRleLoader Source code
Blat Source code
BlocksToPFM Source code Source code
BroadPeakReader Source code
Cell_Cycle_Scoring Source code
CharList2DF Source code
Check_Seurat Source code
ChipSeqRangeUnion Source code
ChrFilter Source code
CisgenomeReader Source code
ClustalO Source code
Colnamer Source code
CombineCoverage Source code
CountNormGenome Source code
CountOverlaps Source code
CpGDesignator Source code
Creator Source code
DESeq_Results Source code
DGE.fisher Source code Source code
DGE.sig Source code Source code
DGE.sig.cum Source code Source code
DateNamer Source code
Dater Source code
DefineRegionBorders Source code
Designator Source code
DrawHeatmapClusters Source code
Enrichr_all Source code
EnsemblExonsTOGtf Source code
ExportCoverage Source code
ExportCoverageChr Source code
ExportReader Source code
ExportToRdata Source code
First Source code
FlatPeaksCenter Source code
FormatEnsembl Source code
GCoords Source code
GRangesToBed Source code
GRangesTodata.frame Source code
GTFGetAnnotation Source code
GappedBamReader Source code
GenomeLoader Source code Source code
GenomicRegionMaker Source code
GetAnnotOverlaps Source code
GetColors Source code
GetFolds Source code
GetMappingStats Source code
GetOverlaps Source code Source code
GetReads Source code
GetRegs Source code
GetTrimmingStats Source code
Get_Affy_Annotation Source code
GffToBed Source code
GtfSelectTranscript Source code
HexamerCorrectionCalculate Source code
HugeFileLoader Source code
Imprint_Scoring Source code
MakeBinaryContrasts Source code
MakeGeneModels Source code
MakeSlidingWindows Source code
MakeTillingWindows Source code
MapQualFilter Source code
MappingStats_Bowtie Source code
MappingStats_Bowtie2 Source code
MappingStats_STAR Source code
MappingStats_Salmon Source code
MarkovBackground Source code
MatchPWM.Large Source code
MemeBlocks Source code
MemeParser Source code
MergeDataTable Source code
MotifHeatmap Source code
NearEdgeReadRemover Source code
PFMparser Source code Source code
PFMtoPSSM Source code
PFMtoPWM Source code
PSSM.Wasserman.Sandelin Source code
PWMScore Source code
Paraclu Source code
ParseFeatures Source code
ParseGenbank Source code
ParseSequence Source code
Parse_MogeneGEO Source code
PeakFinder Source code
PeakRegionMaker Source code
PeakRegionsToFasta Source code
PeakScoreToRank Source code
Percentager Source code
PlotClusters Source code
PlotPCA Source code
Process_Seurat Source code
RandomRemover Source code
ReadAlignedBedFilter Source code
ReadGTFAnnotation Source code
ReadQualFilter Source code
ReadQualFinder Source code
RegionCleaner Source code
RegionCorrector Source code
RepeatMaskerToGRanges Source code
Sample_FindRegion Source code
ScanPWM Source code
SetOverlapFinder Source code
StandardChipseqLoader Source code
Subset_Genes_Seurat Source code
Subset_Seurat Source code
Summarize_Motif_Hits Source code
SwemblReader Source code
TillingWindow Source code
TillingWindowMax Source code
TrimmingStats_BBduk Source code
UCSC.hg.ChrCleaner Source code
UCSC2Reader Source code
UCSCEnsReader Source code
UCSCRefReader Source code
Uniquer Source code
WriteAbstract Source code
WriteBed Source code
WriteRegs Source code
WriteRegsToBed Source code
Zscore Source code
addLetter Source code
annotateDECOD Source code
annotate_Antisense Source code
annotate_Refseq Source code
annotate_deepbind Source code
annotate_tomtom Source code
bed.to.genomeInt Source code
bed.to.genomeInt.strand Source code
cacheFile Source code
calculate_kmers Source code
call_MACS2 Source code
center Source code
check_DNAStringSet_Name Source code Source code
chrFinder Source code
chrSeqlevels Source code
chrStats Source code
clusterFeaturesBED Source code Source code
clusterFeaturesBED.sinfo Source code
clustergram Source code
collect.garbage Source code Source code
combine_Enrichr Source code
compare_Clusters Source code
containedIntervals Source code Source code
convertToBED Source code Source code
copy_Private Source code
copy_Public Source code
copy_Public_DT Source code
copy_Public_rds Source code
corrRemover Source code
decorator Source code
define_Clusters Source code Source code
delayed_decorate Source code
diffAll Source code Source code
diffCol Source code Source code
diffMark Source code Source code
diffNum Source code Source code
diffSel Source code Source code
diffTab Source code Source code
difflog Source code
dinucleotideShuffle Source code
dtfindOverlaps Source code
extract_Jaspar_Motifs Source code
featureContainBED.strand Source code Source code
featureOverlapBED Source code Source code
featureOverlapBED.para Source code Source code
featureOverlapBED.strand Source code Source code
featureOverlapBED.strand.para Source code Source code
fetchAnnotation Source code
fetchGoogleSheet Source code
fetch_Abstract Source code
fetch_SampleSheet Source code
file_Copy Source code
filterCluster Source code
findRegions Source code
findRegionsGenome Source code
findRegionsRLE Source code
find_Motif_Hits Source code
flipStrand Source code
g.int.clusterBED Source code
g.int.clusterBED.strand Source code
g.int.intersectBED Source code
g.int.nonoverlapBED Source code
g.int.overlapBED Source code
g.int.overlapBED.list Source code
genomeInt.to.bed Source code
genomeInt.to.bed.strand Source code
getMeans Source code
getMeans.DESeqDataSet Source code
getMeans.VST Source code
getPCA Source code
getResults Source code
getResults_limma Source code
get_DifferentialExpression Source code
get_Enrichr Source code
get_Enrichr_list Source code
get_MEME_Output Source code
get_Profile Source code
get_Region_Annotation Source code
get_limma Source code
get_limma_tab Source code
get_tsne Source code
ggheat Source code
ggplotScatter Source code
hh Source code
ht Source code
istFiller Source code
ks.default Source code
last Source code
letterA Source code
letterC Source code
letterG Source code
letterT Source code
list.bamfiles Source code
list.bwfiles Source code
list_star.logfiles Source code
ln Source code
ls.objects Source code
lsos Source code
makeBinaryContrasts Source code
makeContlist Source code
makePWM Source code
many_kmeans Source code
markExonNumber Source code
multiplot Source code
nucleotideShuffle Source code
numlist Source code
orderSeqnames Source code
overlappingIntervals Source code Source code
parseSalmonLog Source code
parseSalmonStat Source code
parse_BCFstats Source code
parse_BCFstats_Files Source code
parse_FastQC Source code
parse_FastQCfile Source code
parse_MEMEdb Source code
parse_ScanGenome Source code
parse_dreme Source code
plot.clustergram Source code
plotDESeqDiagnostics Source code
plotLogo Source code
plot_Annotate_Bamfiles Source code
plot_Enrichr Source code
plot_MappingStats Source code
plot_Profile Source code
plot_TrimmingStats Source code
plot_tsne Source code
prepare.mx Source code
prepare.revcom.mx Source code
prepare_snRNA_Reads Source code
prettify Source code
pretty_code Source code
print.decorated Source code
pwm2cons Source code
pwm2ic Source code
readDECOD Source code
readRDS_Integration Source code
read_Annotation Source code
read_ERCC Source code
read_MEME Source code
read_MEME_Output Source code
read_rds_remote Source code
read_rds_remote_file Source code
read_xlsx_remote Source code
reducer Source code
regionError Source code
resizeReads Source code
runDECOD Source code
run_BBduk2 Source code
run_MAST Source code
run_MEME Source code
run_Paraclu Source code
run_SmoothTest Source code
run_Swembl Source code
run_Trimming_BBduk2 Source code
run_deepbind Source code
run_dreme Source code
run_kmerTSNE Source code
run_tomtom Source code Source code
scan_Genome Source code
select_Enrichr Source code
select_Profile Source code
smoothKmers Source code
smoothKmersTime Source code
smoothKmers_plot Source code
source.lib Source code
source.pro Source code
split.numlist Source code
stats_Salmon Source code
summarize_tomtom Source code
test_Enrichr Source code
test_Functions_Pubmed.R Source code
test_Swembl Source code
writePWM Source code Source code
frenkiboy/MyLib documentation built on Oct. 18, 2018, 12:07 p.m.