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TileMap specifications

Information


Unique identifier OMICS_00812
Name TileMap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Output data The output of tilemap includes files which provide summary statistics for each probe, a file which reports regions of interest, and a file which sorts the reported regions from high to low significance level. Files can be uploaded directly to UCSC genome browser to visualize the reported regions.
Output format REG, BED, SUM, TXT
Operating system Unix/Linux, Mac OS, Windows
Computer skills Advanced
Version 2.0
Stability Stable
Maintained Yes

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  • person_outline Wing Hung Wong <>

Publication for TileMap

TileMap in publications

 (29)
PMCID: 4711971
PMID: 26760036
DOI: 10.1371/journal.pgen.1005771

[…] http://www.ncbi.nlm.nih.gov/geo/ with accession numbers gse48857 [] and gse8169 [], respectively. peaks for chip-seq data were identified using macs14 [], and chip-chip peaks were identified using tilemap implemented in cisgenome []. for igv viewing [], we normalized h3k27me3 samples such that the numbers of reads in common peak regions between col-0 and pcg mutants are the same. for input […]

PMCID: 4450877
PMID: 26030458
DOI: 10.1371/journal.pone.0126466

[…] and we further verified h3k27me3 and h3k79me3 antibodies using dot blots. for chip-chip, immunoprecipitated dna was amplified, labeled, and hybridized to human 1m promoter tiling arrays (agilent). tilemap was used to define regions with significantly enriched h3k27me3 [], and intensities were normalized to internal standards. peaks were ranked according to their test statistics value (maximal […]

PMCID: 4330375
PMID: 25609699
DOI: 10.1093/nar/gkv011

[…] genomic region, and this was given a binary score of presence or absence of a given chip peak. the coordinates of genomic regions defined as bound by cardiogenic tfs was previously published using tilemap (). the coordinates of genomic regions defined as enriched for a particular histone modification were identified using macs (tsize = 36, shift size = 90, bw = 100, gsize = 135 000 000) […]

PMCID: 4146391
PMID: 24961800
DOI: 10.1242/dev.101956

[…] genechip drosophila tiling array 1.0r, as described ()., bioinformatics analysis was performed as described (). after data normalization, significantly enriched regions were determined using tilemap (). for each significant region, the chip peak was calculated and crms defined as a 200 bp region centered around the peak (). all chip raw data are available in arrayexpress [accession […]

PMCID: 3532402
PMID: 23285203
DOI: 10.1371/journal.pone.0052855

[…] (geo), accession number gse7907., signal intensities [perfect match (pm)-mismatch (mm)] from two independent biological replicates were quantile-normalized after log2-transformation using the tilemap package . subsequently, signals from ip and input dna were linearly scaled to the same mean. a log ratio of the average ip to input value was calculated for each probe. the normalized signals […]


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TileMap institution(s)
Department of Statistics, Harvard University Cambridge, MA, USA; Department of Statistics, Stanford University Stanford, CA, USA
TileMap funding source(s)
The work was partially supported by NIH grant GM-067250.

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