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See:
Description
Class Summary | |
AverageDoubles | Slides a 50 index window along an array averaging the contents. |
Bar2Gr | Utility to convert simple one graph xxx.bar files to xxx.gr files. |
Bed2Gr | Converts a bed file to multiple gr files. |
CalcGCAndTransform | Parses out treatment and control oligo info from intervals, calculate GC and transform ratios based on GC corrector,
see TransformRatios . |
CalcGCRatiosFromIntervals | Parse out treatment and control oligo info from intervals, calculate GC and ratios to look for bias. |
ConvertAgilentData | Reads in an Agilent tiling data file and outputs a tpmap and four cela files. |
ConvertGeoData | Reads and parses in a GEO data file into a tpmap and xxx.cela files for TiMAT2 processing. |
ConvertNimblegenNDF2TPMap | Converts a Nimblegen NDF txt file to a tpmap.! |
ConvertNimblegenPAIR2Cela | Converts Nimblegen PAIR txt files to a cela files.! |
CorrelateGrFiles | |
GCRatio | Container for a ratio and associated %GC content for a particular oligo. |
Gr2Bar | |
GrGraph | Container for holding info related to a xxx.gr file. |
InefficientPseudoMedian | |
PrependColumn | |
Regions2Intervals | Converts binding regions to intervals setting the binding region as the best window and adds 2kb on either side. |
ScoredRegionsFormatFixer | Converts a file format to something usable by Excel from the joinRegionsWithScores.sh script. |
Sgr2Bar | |
SgrComparator | |
TextPValOrSig2Gr | Converts a bed file to multiple gr files. |
TransformRatios | Transforms ratio scores in Intervals based on the BAC GC Corrector. |
Util | Static helper methods for all things Affy |
WindowHistogram | Makes a histogram of scores from a Window[]. |
Rough working scripts.
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