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PHeatmaps specifications

Information


Unique identifier OMICS_26726
Name PHeatmaps
Alternative names Pretty Heatmaps, pheatmap
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License GNU General Public License version 2.0
Computer skills Advanced
Version 1.0.9
Stability Stable
Maintained Yes

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Maintainer


  • person_outline Raivo Kolde <>

Additional information


https://cran.r-project.org/web/packages/pheatmap/index.html

PHeatmaps in pipelines

 (102)
2018
PMCID: 5792552
PMID: 29386661
DOI: 10.1038/s41598-018-20419-9

[…] as follows log2 (fpkmamrz) − log2(fpkmf113). p. fluorescens f113 genes annotated as encoding diguanylate cyclases and phosphodiesterases were selected to prepare the heatmap expression figure with pheatmap r package., rna-seq raw data have been deposited at ncbi as bioproject prjna419480., , electronic supplementary material , supplementary information accompanies this paper […]

2018
PMCID: 5802717
PMID: 29410526
DOI: 10.1038/s41598-018-20935-8

[…] of the p-value after normalization (padj, qvalue) was set as ≤0.05 for filtering accurate degs. the clustering of degs was analysed based on fpkm value with the use of ggplot2 (version 2.1.0) and pheatmap (version 1.0.8)., gene ontology (go) and kyoto encyclopedia of genes and genomes (kegg) pathway enrichment analysis of degs:goseq (r bioconductor package) based on wallenius non-central […]

2018
PMCID: 5850119
PMID: 29568492
DOI: 10.5256/f1000research.14748.r30355

[…] following line to install packages #bioclite(c("clusterprofiler", "deseq2", "genomicfeatures", "genomicinteractions", "genomicranges", "ggplot2", "gviz", "gwascat", "interactionset", "recount", "pheatmap", "rcolorbrewer", "rtracklayer", "r.utils", "splitstackshape", "variantannotation")) , we start with a common scenario: we ran a rna-seq experiment comparing patients with a disease […]

2018
PMCID: 5856545
PMID: 29483267
DOI: 10.1073/pnas.1719455115

[…] in gene expression, logcpm is logarithm of counts per million reads, p value is p value, fdr is false discovery rate, and tair symbol is known gene name. heatmap plots were generated by the pheatmap package in r., leaf tissue was fixed in 2% (vol/vol) glutaraldehyde plus 2% (vol/vol) paraformaldehyde in 70 mm pipes buffer, ph 6.8, for 1 h at room temperature, then washed and postfixed […]

2018
PMCID: 5863495
PMID: 29600195
DOI: 10.3389/fcimb.2018.00045

[…] al., ), and the raw counts were processed using deseq2 package in r (love et al., ). the downstream analysis and plotting was done using home brew scripts written in r (r archive network). r package pheatmap was employed for the heatmap where the values were scaled according to row to depict how the gene expression for the specific gene changed across the conditions., l. interrogans serovar […]


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PHeatmaps in publications

 (530)
PMCID: 5959866
PMID: 29777171
DOI: 10.1038/s41467-018-04329-y

[…] was carried out with deseq2. for the visualization of gene expression and unsupervised hierarchical clustering of the samples the rlog normalization in deseq2 was applied. we used the r library pheatmap for sample clustering (euclidian distance, complete linkage clustering) and heatmap.2 from the gplots package to visualize differentially expressed genes (pearson correlation and ward.d […]

PMCID: 5956100
PMID: 29769607
DOI: 10.1038/s41598-018-25998-1

[…] of p ≤ 0.05, with a fold change ≥1.5, between any two consecutive time points. principal component analysis was performed using the prcomp function in r software. heatmaps were generated using the pheatmap package in r software. signed difference ratios (sdr) were calculated similar to, except the average for each gene across all samples was subtracted from each sample. fastq sequences […]

PMCID: 5954203
DOI: 10.1128/mSystems.00205-17

[…] significant correlations were defined as a correlation coefficient (r) of over 0.05 (or less than −0.05), with a pseudo-p value of ≤0.05 (). heatmaps of the correlation were generated in r using the pheatmap package. we performed hierarchical clustering for both columns and rows with the average linkage method using pearson’s correlation. we utilized picrust v1.0.0 to construct a predicted […]

PMCID: 5951918
PMID: 29760424
DOI: 10.1038/s41467-018-04215-7

[…] a list of 72 genes of interest was used for clustering by multidimensional scaling using the base r package stats. spearman correlation based on those 72 genes of interest was performed using the pheatmap package. fpkm values for each cell were median-normalized and used for spearman correlation based on the expression of the same set of genes of interest. for the tenfold enrichment analysis, […]

PMCID: 5954288
PMID: 29764387
DOI: 10.1186/s12864-018-4457-8

[…] to perform hierarchical clustering. the normalized rptm values plus one were log scaled to calculate correlation coefficient (cc) values between samples. then the cc values were applied to the pheatmap function in the pheatmap library in r to perform hierarchical clustering. mirnas with average abundances of at least 5 rptm in the 14 samples were used to perform principle component […]


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