Genome Contact Map Explorer - gcMapExplorer
latest
Requirements and Installation
How to use gcMapExplorer?
Genome Contact Map Browser
About file formats
Normalization of Hi-C maps
Frequently asked questions
Download example datasets
Summary of Python Modules
Examples using Python Modules
Python Modules documentation
Genome Contact Map Explorer - gcMapExplorer
Docs
»
Index
Edit on GitHub
Index
_
|
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
J
|
K
|
L
|
M
|
N
|
O
|
P
|
R
|
S
|
T
|
U
|
W
|
X
|
Y
_
_bigWigtoWig() (BigWigHandler method)
_checkBigWigInfoProgram() (BigWigHandler method)
(EncodeDatasetsConverter method)
_checkBigWigToWigProgram() (BigWigHandler method)
(EncodeDatasetsConverter 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)
_readFromCheckPoint() (EncodeDatasetsConverter method)
_removeBigWigFiles() (EncodeDatasetsConverter method)
_removeTempNumpyFile() (TextFileHandler method)
_saveChromSizeAndIndex() (BEDHandler method)
(WigHandler method)
_StoreInHdf5File() (BEDHandler method)
(WigHandler method)
_writeToCheckPoint() (EncodeDatasetsConverter method)
A
addCCMap2GCMap() (in module gcMapExplorer.lib.gcmap)
addChromSizeInfo() (TempNumpyArrayFiles method)
addDataByArray() (HDF5Handler method)
arr (MemoryMappedArray attribute)
arrays (TempNumpyArrayFiles attribute)
assembly (EncodeDatasetsConverter 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.util)
BinsNContactFilesHandler (class in gcMapExplorer.lib.importer)
bLog (CCMAP attribute)
(GCMAP attribute)
bNoData (CCMAP attribute)
(GCMAP attribute)
buildDataTree() (HDF5Handler method)
C
calculateCorrelation() (in module gcMapExplorer.lib.corrMatrix)
calculateCorrMatrix() (in module gcMapExplorer.lib.corrMatrix)
calculateCorrMatrixForCCMap() (in module gcMapExplorer.lib.corrMatrix)
calculateCorrMatrixForGCMaps() (in module gcMapExplorer.lib.corrMatrix)
calculateCovariance() (in module gcMapExplorer.lib.corrMatrix)
calculateCovMatrix() (in module gcMapExplorer.lib.corrMatrix)
calculateTransitionProbabilityMatrix() (in module gcMapExplorer.lib.statDist)
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)
checkCCMapObjectOrFile() (in module gcMapExplorer.lib.ccmap)
checkMapExist() (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)
cleanScratch() (in module gcMapExplorer.config)
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 (MemoryMappedArray attribute)
copy() (CCMAP method)
copy_from (MemoryMappedArray attribute)
copy_to (MemoryMappedArray attribute)
correlateCMaps() (in module gcMapExplorer.lib.cmstats)
correlateGCMaps() (in module gcMapExplorer.lib.cmstats)
D
data (HDF5Handler attribute)
(TextFileHandler attribute)
dejsonify() (in module gcMapExplorer.lib.ccmap)
detectOutliers1D() (in module gcMapExplorer.lib.util)
detectOutliersMasked1D() (in module gcMapExplorer.lib.util)
downloadMetaData() (EncodeDatasetsConverter method)
downSample2DMap() (in module gcMapExplorer.lib.ccmap)
downsampleAllMapToResolution() (GCMAP method)
downSampleCCMap() (in module gcMapExplorer.lib.ccmap)
downsampleMapToResolution() (GCMAP method)
dtype (CCMAP attribute)
(GCMAP attribute)
(MemoryMappedArray attribute)
E
EncodeDatasetsConverter (class in gcMapExplorer.lib.genomicsDataHandler)
export_cmap() (in module gcMapExplorer.lib.ccmap)
F
filename (HDF5Handler attribute)
(TextFileHandler attribute)
fileOpened (GCMAP attribute)
files (TempNumpyArrayFiles attribute)
fillAllArraysWithZeros() (TempNumpyArrayFiles method)
filterReplicates() (EncodeDatasetsConverter method)
finestResolution (GCMAP attribute)
fIns (HomerInputHandler attribute)
fTmpOut (HomerInputHandler attribute)
fTmpOutNames (HomerInputHandler attribute)
G
GCMAP (class in gcMapExplorer.lib.gcmap)
gcMapExplorer (module)
gcMapExplorer.config (module)
gcMapExplorer.lib.ccmap (module)
gcMapExplorer.lib.ccmapHelpers (module)
gcMapExplorer.lib.cmstats (module)
gcMapExplorer.lib.corrMatrix (module)
gcMapExplorer.lib.gcmap (module)
gcMapExplorer.lib.importer (module)
gcMapExplorer.lib.normalizer (module)
gcMapExplorer.lib.statDist (module)
gcMapExplorer.lib.util (module)
gcmapOut (PairCooMatrixHandler attribute)
gcmapOutOptions (PairCooMatrixHandler attribute)
gen_map_from_locations_value() (in module gcMapExplorer.lib.importer)
generateAllTempNumpyFiles() (TempNumpyArrayFiles method)
generateTempNumpyFile() (TempNumpyArrayFiles method)
genMapNameList() (GCMAP 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)
getConfig() (in module gcMapExplorer.config)
getDataNameList() (HDF5Handler method)
getOutputShapeFor2DMapDownsampling() (in module gcMapExplorer.lib.ccmap)
getRandomName() (in module gcMapExplorer.lib.util)
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 (EncodeDatasetsConverter attribute)
(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)
kth_diag_indices() (in module gcMapExplorer.lib.util)
L
load_ccmap() (in module gcMapExplorer.lib.ccmap)
loadGCMapAsCCMap() (in module gcMapExplorer.lib.gcmap)
loadSmallestMap() (GCMAP method)
locate_significant_digit_after_decimal() (in module gcMapExplorer.lib.util)
M
make_editable() (CCMAP method)
make_readable() (CCMAP method)
make_unreadable() (CCMAP method)
make_writable() (CCMAP method)
mapNameList (GCMAP attribute)
MapNotFoundError
(class in gcMapExplorer.lib.util)
mapType (CooMatrixHandler attribute)
(GCMAP attribute)
matrix (CCMAP attribute)
(GCMAP attribute)
MatrixPowerRAM() (in module gcMapExplorer.lib.statDist)
maxEntryWrite (BEDHandler attribute)
(BigWigHandler attribute)
(WigHandler attribute)
maxvalue (CCMAP attribute)
(GCMAP attribute)
MemoryMappedArray (class in gcMapExplorer.lib.ccmapHelpers)
metafile (EncodeDatasetsConverter attribute)
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)
normalizeCCMapByVCNorm() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByIC() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByKR() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByMCFS() (in module gcMapExplorer.lib.normalizer)
normalizeGCMapByVCNorm() (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)
(EncodeDatasetsConverter attribute)
pathTobigWigToWig (BigWigHandler attribute)
(EncodeDatasetsConverter attribute)
performDownSampling() (GCMAP method)
printConfig() (in module gcMapExplorer.config)
R
readData() (TextFileHandler method)
readMetaData() (EncodeDatasetsConverter method)
remove_zeros() (in module gcMapExplorer.lib.ccmapHelpers)
resolution (CooMatrixHandler attribute)
(GCMAP attribute)
(HomerInputHandler attribute)
ResolutionNotFoundError
(class in gcMapExplorer.lib.util)
resolutionToBinsize() (in module gcMapExplorer.lib.util)
run (KnightRuizNorm attribute)
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)
(EncodeDatasetsConverter 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)
sorted_nicely() (in module gcMapExplorer.lib.util)
statDistrByEigenDecompForCCMap() (in module gcMapExplorer.lib.statDist)
statDistrByEigenDecompForGCMap() (in module gcMapExplorer.lib.statDist)
state (CCMAP attribute)
stationaryDistributionByEigenDecomp() (in module gcMapExplorer.lib.statDist)
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)
transitionProbabilityMatrixForCCMap() (in module gcMapExplorer.lib.statDist)
transitionProbabilityMatrixForGCMap() (in module gcMapExplorer.lib.statDist)
U
updateArraysByBigWig() (TempNumpyArrayFiles method)
updateArraysByChromSize() (TempNumpyArrayFiles method)
updateConfig() (in module gcMapExplorer.config)
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)
Read the Docs
v: latest
Versions
latest
stable
Downloads
htmlzip
epub
On Read the Docs
Project Home
Builds
Free document hosting provided by
Read the Docs
.