Genome Contact Map Explorer - gcMapExplorer
stable
Requirements and Installation
How to use gcMapExplorer?
Genome Contact Map Browser
About gcmap file
About ccmap and npbin files
About Genomic track h5 file
Normalization of Hi-C maps
Download example datasets
Summary of Python Modules
Examples using Python Modules
Python Modules documentation
Genome Contact Map Explorer - gcMapExplorer
Docs
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Index
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Index
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B
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C
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D
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_bigWigtoWig() (BigWigHandler method)
_chromPointerInFile (BEDHandler attribute)
(WigHandler attribute)
_FillDataInNumpyArrayFile() (BEDHandler method)
(WigHandler method)
_generateTempNumpyFile() (TempNumpyArrayFiles method)
(TextFileHandler method)
_getBigWigInfo() (BigWigHandler method)
(TempNumpyArrayFiles method)
_getBinSize() (TextFileHandler method)
_getChromSizeInfo() (BEDHandler method)
(WigHandler method)
_getChromTitle_parseWig() (WigHandler method)
_getChromTitleBedgraph_parseWig() (WigHandler method)
_getSpan_parseWig() (WigHandler method)
_getStartStepFixedStep_parseWig() (WigHandler method)
_loadChromSizeAndIndex() (BEDHandler method)
(WigHandler method)
_parseBed() (BEDHandler method)
_parseWig() (WigHandler method)
_PerformDataCoarsening() (BEDHandler method)
(WigHandler method)
_removeTempNumpyFile() (TextFileHandler method)
_saveChromSizeAndIndex() (BEDHandler method)
(WigHandler method)
_StoreInHdf5File() (BEDHandler method)
(WigHandler method)
A
addCCMap2GCMap() (in module gcMapExplorer.lib.gcmap)
addChromSizeInfo() (TempNumpyArrayFiles method)
addDataByArray() (HDF5Handler method)
arr (MemoryMappedArray attribute)
arrays (TempNumpyArrayFiles attribute)
B
BedFileNames (BEDHandler attribute)
BEDHandler (class in gcMapExplorer.lib.genomicsDataHandler)
bigWigFileNames (BigWigHandler attribute)
BigWigHandler (class in gcMapExplorer.lib.genomicsDataHandler)
bigWigtoWig() (BigWigHandler method)
binFile (BinsNContactFilesHandler attribute)
binsize (BinsNContactFilesHandler attribute)
(CCMAP attribute)
(GCMAP attribute)
(TextFileHandler attribute)
binsizes (GCMAP attribute)
binsizeToResolution() (in module gcMapExplorer.lib.ccmap)
BinsNContactFilesHandler (class in gcMapExplorer.lib.importer)
bLog (CCMAP attribute)
(GCMAP attribute)
bNoData (CCMAP attribute)
(GCMAP attribute)
buildDataTree() (HDF5Handler method)
C
CCMAP (class in gcMapExplorer.lib.ccmap)
ccmapOutDir (PairCooMatrixHandler attribute)
ccmaps (BinsNContactFilesHandler attribute)
ccmapSuffix (PairCooMatrixHandler attribute)
changeGCMapCompression() (in module gcMapExplorer.lib.gcmap)
changeMap() (GCMAP method)
changeResolution() (GCMAP method)
ChromBinsInfo (BinsNContactFilesHandler attribute)
chromList (HomerInputHandler attribute)
chromName (BEDHandler attribute)
(BigWigHandler attribute)
(WigHandler attribute)
ChromSize (BinsNContactFilesHandler attribute)
chromSizeInfo (BEDHandler attribute)
(BigWigHandler attribute)
(TempNumpyArrayFiles attribute)
(WigHandler attribute)
close() (HDF5Handler method)
column (BEDHandler attribute)
compressHandle (CooMatrixHandler attribute)
(HomerInputHandler attribute)
compressType (CooMatrixHandler attribute)
(HomerInputHandler attribute)
contactFile (BinsNContactFilesHandler attribute)
CooMatrixHandler (class in gcMapExplorer.lib.importer)
coordinate (CooMatrixHandler attribute)
copy() (CCMAP method)
(MemoryMappedArray method)
copy_from() (MemoryMappedArray method)
copy_to() (MemoryMappedArray method)
correlateCMaps() (in module gcMapExplorer.lib.cmstats)
D
data (HDF5Handler attribute)
(TextFileHandler attribute)
dejsonify() (in module gcMapExplorer.lib.ccmap)
dtype (CCMAP attribute)
(GCMAP attribute)
(MemoryMappedArray attribute)
E
export_cmap() (in module gcMapExplorer.lib.ccmap)
F
filename (HDF5Handler attribute)
(TextFileHandler attribute)
fileOpened (GCMAP attribute)
files (TempNumpyArrayFiles attribute)
fillAllArraysWithZeros() (TempNumpyArrayFiles method)
finestResolution (GCMAP attribute)
fIns (HomerInputHandler attribute)
fTmpOut (HomerInputHandler attribute)
fTmpOutNames (HomerInputHandler attribute)
G
GCMAP (class in gcMapExplorer.lib.gcmap)
gcMapExplorer (module)
gcMapExplorer.lib.ccmap (module)
gcMapExplorer.lib.ccmapHelpers (module)
gcMapExplorer.lib.cmstats (module)
gcMapExplorer.lib.gcmap (module)
gcMapExplorer.lib.importer (module)
gcMapExplorer.lib.normalizer (module)
gcmapOut (PairCooMatrixHandler attribute)
gcmapOutOptions (PairCooMatrixHandler attribute)
gen_map_from_locations_value() (in module gcMapExplorer.lib.importer)
generateTempNumpyFile() (TempNumpyArrayFiles method)
genMapNameList() (GCMAP method)
genrateAllTempNumpyFiles() (TempNumpyArrayFiles method)
get_nonzeros_index() (in module gcMapExplorer.lib.ccmapHelpers)
get_ticks() (CCMAP method)
(GCMAP method)
getAvgContactByDistance() (in module gcMapExplorer.lib.cmstats)
getBigWigInfo() (BigWigHandler method)
getChromList() (HDF5Handler method)
getDataNameList() (HDF5Handler method)
getRawWigDataAsDictionary() (BEDHandler method)
(WigHandler method)
getResolutionList() (HDF5Handler method)
groupName (GCMAP attribute)
H
hasChromosome() (HDF5Handler method)
hasDataName() (HDF5Handler method)
hasResolution() (HDF5Handler method)
hdf5 (GCMAP attribute)
(HDF5Handler attribute)
HDF5Handler (class in gcMapExplorer.lib.genomicsDataHandler)
HomerInputHandler (class in gcMapExplorer.lib.importer)
I
indexFile (BEDHandler attribute)
(WigHandler attribute)
inputCompressedFile (CooMatrixHandler attribute)
(HomerInputHandler attribute)
inputFile (PairCooMatrixHandler attribute)
inputFileList (CooMatrixHandler attribute)
(HomerInputHandler attribute)
inputType (CooMatrixHandler attribute)
(HomerInputHandler attribute)
isBedParsed (BEDHandler attribute)
isWigParsed (WigHandler attribute)
J
jsonify() (in module gcMapExplorer.lib.ccmap)
K
KnightRuizNorm (class in gcMapExplorer.lib.normalizeKnightRuiz)
L
load_ccmap() (in module gcMapExplorer.lib.ccmap)
loadGCMapAsCCMap() (in module gcMapExplorer.lib.gcmap)
loadSmallestMap() (GCMAP method)
M
make_editable() (CCMAP method)
make_readable() (CCMAP method)
make_unreadable() (CCMAP method)
make_writable() (CCMAP method)
mapNameList (GCMAP attribute)
mapType (CooMatrixHandler attribute)
(GCMAP attribute)
matrix (CCMAP attribute)
(GCMAP attribute)
maxEntryWrite (BEDHandler attribute)
(BigWigHandler attribute)
(WigHandler attribute)
maxvalue (CCMAP attribute)
(GCMAP attribute)
MemoryMappedArray (class in gcMapExplorer.lib.ccmapHelpers)
methodToCombine (BEDHandler attribute)
(BigWigHandler attribute)
(WigHandler attribute)
minvalue (CCMAP attribute)
(GCMAP attribute)
N
normalizeCCMapByIC() (in module gcMapExplorer.lib.normalizer)
normalizeCCMapByKR() (in module gcMapExplorer.lib.normalizer)
normalizeCCMapByMCFS() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByIC() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByKR() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByMCFS() (in module gcMapExplorer.lib.normalizer)
NormalizeKnightRuizOriginal() (in module gcMapExplorer.lib.normalizer)
npyBinFileList (BinsNContactFilesHandler attribute)
O
open() (HDF5Handler method)
outputFileList (CooMatrixHandler attribute)
P
PairCooMatrixHandler (class in gcMapExplorer.lib.importer)
parseBed() (BEDHandler method)
parseWig() (WigHandler method)
path2matrix (CCMAP attribute)
(MemoryMappedArray attribute)
pathTobigWigInfo (BigWigHandler attribute)
pathTobigWigToWig (BigWigHandler attribute)
performDownSampling() (GCMAP method)
R
readData() (TextFileHandler method)
remove_zeros() (in module gcMapExplorer.lib.ccmapHelpers)
resolution (CooMatrixHandler attribute)
(GCMAP attribute)
(HomerInputHandler attribute)
resolutionToBinsize() (in module gcMapExplorer.lib.ccmap)
run() (KnightRuizNorm method)
runConversion() (PairCooMatrixHandler method)
S
save_ccmap() (in module gcMapExplorer.lib.ccmap)
save_ccmaps() (BinsNContactFilesHandler method)
(CooMatrixHandler method)
(HomerInputHandler method)
save_gcmap() (BinsNContactFilesHandler method)
(CooMatrixHandler method)
(HomerInputHandler method)
saveAsH5() (BEDHandler method)
(BigWigHandler method)
(WigHandler method)
setChromosome() (BEDHandler method)
(WigHandler method)
setGCMapOptions() (PairCooMatrixHandler method)
setLabels() (CooMatrixHandler method)
setOutputFileList() (CooMatrixHandler method)
setTitle() (HDF5Handler method)
shape (CCMAP attribute)
(GCMAP attribute)
(TextFileHandler attribute)
state (CCMAP attribute)
T
TempNumpyArrayFiles (class in gcMapExplorer.lib.genomicsDataHandler)
TextFileHandler (class in gcMapExplorer.lib.genomicsDataHandler)
title (CCMAP attribute)
(GCMAP attribute)
(HDF5Handler attribute)
(TextFileHandler attribute)
tmpNumpyArrayFiles (BEDHandler attribute)
(WigHandler attribute)
tmpNumpyFileName (TextFileHandler attribute)
toCoarserResolution() (GCMAP method)
toFinerResolution() (GCMAP method)
U
updateArraysByBigWig() (TempNumpyArrayFiles method)
updateArraysByChromSize() (TempNumpyArrayFiles method)
W
WigFileNames (BigWigHandler attribute)
(WigHandler attribute)
wigHandle (BigWigHandler attribute)
WigHandler (class in gcMapExplorer.lib.genomicsDataHandler)
workDir (CooMatrixHandler attribute)
(HomerInputHandler attribute)
(MemoryMappedArray attribute)
(PairCooMatrixHandler attribute)
(TempNumpyArrayFiles attribute)
(TextFileHandler attribute)
X
xlabel (CCMAP attribute)
(GCMAP attribute)
xticks (CCMAP attribute)
(GCMAP attribute)
Y
ylabel (CCMAP attribute)
(GCMAP attribute)
yticks (CCMAP attribute)
(GCMAP attribute)
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