MAnorm statistics

To access cutting-edge analytics on consensus tools, life science contexts and associated fields, you will need to subscribe to our premium service.

Subscribe
info

Citations per year

Citations chart
info

Popular tool citations

chevron_left Normalization Differential peak calling chevron_right
Popular tools chart
info

Tool usage distribution map

Tool usage distribution map
info

Associated diseases

Associated diseases

Protocols

To access compelling stats and trends, optimize your time and resources and pinpoint new correlations, you will need to subscribe to our premium service.

Subscribe

MAnorm specifications

Information


Unique identifier OMICS_00467
Name MAnorm
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages MATLAB, R
Computer skills Advanced
Stability Stable
Maintained Yes

Versioning


Add your version

Maintainers


  • person_outline Stuart Orkin <>
  • person_outline David Waxman <>

Publication for MAnorm

MAnorm in pipelines

 (7)
2017
PMCID: 5385585
PMID: 28387316
DOI: 10.1038/ncomms14922

[…] default values for other parameters. computer code is available upon request. quantitative differences of histone modification between adc and scc tumours from kras/lkb1 mice were analysed using the manorm algorithm with a p-value cutoff of 10−10 and >1 log2 fold change for h3k4me3 and h3k27ac., wiggle files with a 10 bp resolution for h3k4me3, h3k27ac and h3k27me3 modifications […]

2017
PMCID: 5606996
PMID: 28931805
DOI: 10.1038/s41467-017-00353-6

[…] ated with dop and 29 496 peaks for the untreated samples. to measure the relative changes in read densities of the h3k9ac peaks, we compared detected peaks from treated and untreated conditions using manorm software. manorm software normalizes peak intensities, then calculates an m-value for each peak that is representative of the relative peak intensity between two conditions (q-value < 0.05). […]

2017
PMCID: 5660450
PMID: 29078804
DOI: 10.1186/s13073-017-0481-6

[…] approaches macs (model-based analysis for chip-seq) and sicer (spatial clustering approach for the identification of chip-enriched regions) [–]. differential binding peaks were obtained by software manorm as described []. functional classification of refined data for peak-related genes was performed using ncbi gene resource (bethesda, md, usa). all hit classification diagrams were made […]

2017
PMCID: 5778473
PMID: 29126117
DOI: 10.1093/nar/gkx1052

[…] only peak regions (±250 bp from the peak summit) outside ±1 kb of tsss (termed distal peaks) were used, and a maximum of 3000 peak regions from the lowest p-values (p < 0.01) were chosen via manorm analysis. these sequences were extracted using the table browser (). relative locations of peak regions were analyzed using great with default settings ()., data analysis for rna-seq […]

2016
PMCID: 4987520
PMID: 27507714
DOI: 10.1038/ncomms12376

[…] (illumina) to obtain 50-bp-long reads. demultiplexing was carried out using in-house unix shell script followed by mapping to mouse genome (mm9) using bowtie. peaks were identified with macs, and manorm analysis was used to identify differentially accessible regions between control myeloid and pre-b cells, as well as control and mef2c-deficient pre-b cells or myeloid cells. peaks […]


To access a full list of citations, you will need to upgrade to our premium service.

MAnorm in publications

 (36)
PMCID: 5920086
PMID: 29700302
DOI: 10.1038/s41467-018-04111-0

[…] significance was calculated by deseq2 with a false discover rate (fdr) cutoff of 0.05. for atac-seq experiments, significant differences in enrichment between peaks was determined using an optimized manorm script, with the cutoff set at a minimum fold-change of 2 and significance of p < 0.05., rna-seq, chip-seq, and atac-seq data shown in this study have been deposited in the gene expression […]

PMCID: 5834201
PMID: 29462142
DOI: 10.1371/journal.pgen.1007233

[…] the gm9 and prdx4 loci, which both represent a class of x-linked rnf8-dependent escape genes (). for the quantitative analyses of chip-seq peaks between ps and rs, we used the peak analysis software manorm to compare peaks derived from two pairwise next-generation sequencing datasets []. on the sex chromosomes, h3k4me2 peaks tend to be distributed in promoter and intergenic regions, […]

PMCID: 5763304
PMID: 29322919
DOI: 10.1186/s12918-017-0514-1

[…] predictions., in this section, we are going to investigate the effect of normalization strategy on our proposed hadamard kernel. as most of our datasets are microarray data, we therefore introduce ‘manorm’ which is an embedded function in matlab for microarray data normalization. it scales the values in each column of microarray data matrix, by dividing by the mean column intensity. besides, […]

PMCID: 5738049
PMID: 29262769
DOI: 10.1186/s12859-017-1946-8

[…] the gene expression data in order to have equivalent effect on the two-fold increase or decrease in gene expression data in log-scale. then, the gene expression data is normalized with the help of ‘manorm()’ matlab function to eliminate the inconstancies in microarray experimentation that influenced the observed gene expressions as a consequence of deviation in the experimental process, […]

PMCID: 5727985
PMID: 29233090
DOI: 10.1186/s12864-017-4353-7

[…] commands including bamtobed, genomecoveragebed, bedgraphtobigwig and finally bigwigtowig commands of bedtools [] and ucsc genome browser toolkits []. we then used macs2 [] for peak finding and manorm [] for normalization of genome coverage data. hence the genome coverage values that are depicted in the figures are the normalized total number of ngs reads that are aligned to each genomic […]


To access a full list of publications, you will need to upgrade to our premium service.

MAnorm institution(s)
Departments of Pediatric Oncology and Computational Biology, DanaFarber Cancer Institute, Boston, MA, USA; Division of Pediatric Hematology-Oncology, The Karp Family Research Laboratories, Children’s Hospital, Boston, MA, USA; Division of Cell and Molecular Biology, Department of Biology, Boston University, Boston, MA, USA; Harvard Stem Cell Institute and the Howard Hughes Medical Institute, Children’s Hospital, Boston, MA, USA

MAnorm reviews

star_border star_border star_border star_border star_border
star star star star star

Be the first to review MAnorm