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HTSFilter specifications


Unique identifier OMICS_14779
Name HTSFilter
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
License Artistic License version 2.0
Computer skills Advanced
Version 1.20.0
Stability Stable
methods, stats, graphics, Biobase, utils, testthat, BiocStyle, grDevices, R(>=3.4), edgeR(>=3.9.14), DESeq2(>=1.10.1), DESeq(>=1.22.1), BiocParallel(>=1.4.3), EDASeq(>=2.1.4)
Maintained Yes




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  • person_outline Andrea Rau

Publication for HTSFilter

HTSFilter citations


Dynamic genome wide expression profiling of Drosophila head development reveals a novel role of Hunchback in retinal glia cell development and blood brain barrier integrity

PLoS Genet
PMCID: 5796731
PMID: 29360820
DOI: 10.1371/journal.pgen.1007180

[…] []. a summary of raw read counts mapped to each gene and time point is available at the geo repository (gse94915)., for each pair-wise comparison (72h ael vs. 96h ael and 96h ael vs. 120h ael) htsfilter [] was used with default parameters to filter out genes with very low expression in all samples. for the remaining genes in each pair-wise comparison, differential expression was calculated […]


Sunflower oil supplementation affects the expression of miR 20a 5p and miR 142 5p in the lactating bovine mammary gland

PLoS One
PMCID: 5744907
PMID: 29281677
DOI: 10.1371/journal.pone.0185511

[…] was performed using r version 3.0.1 (r development core team, 2013) with the bioconductor package deseq2 [], as described by le guillou et al. []. data were filtered using the bioconductor package htsfilter []. this method aims to identify the threshold that maximizes the filtering similarity among biological replicates, or in other words that where most genes tend to have either normalized […]


IL 2 imprints human naive B cell fate towards plasma cell through ERK/ELK1 mediated BACH2 repression

Nat Commun
PMCID: 5682283
PMID: 29129929
DOI: 10.1038/s41467-017-01475-7

[…] trimmed using cutadapt 1.0. potential pcr duplicates were removed using samtools 1.3. reads were then aligned on the grch38 human genome using star 2.4.2a. differential expression on filtered genes (htsfilter 1.7.1), were performed using deseq2 in r 3.3.1. genes were declared differentially expressed with a false discovery rate < 5%. for heatmap, genes differentially expressed with fold […]


The neonicotinoid insecticide Clothianidin adversely affects immune signaling in a human cell line

Sci Rep
PMCID: 5647381
PMID: 29044138
DOI: 10.1038/s41598-017-13171-z

[…] (v1.4.5-p1) was used to perform read summarization at gene level, with the strand-specific option “reversely stranded”. statistical analysis of the read counts was performed with r, using the htsfilter package, to remove low expressed genes, and the noiseq package, to perform differential expression analysis. gene ontology enrichment analysis of the differentially expressed genes […]


The hypothesis that Helicobacter pylori predisposes to Alzheimer’s disease is biologically plausible

Sci Rep
PMCID: 5552707
PMID: 28798312
DOI: 10.1038/s41598-017-07532-x

[…] expression counts were then calculated by using featurecounts (version 1.4.6-p5). raw counts were imported in r and, following tmm normalization, the lowly expressed genes were filtered out with the htsfilter package. differential expression analysis of filtered genes was carried out with the noiseq package. gene ontology enrichment analysis of differentially expressed genes was carried […]


Long noncoding RNA repertoire in chicken liver and adipose tissue

PMCID: 5225574
PMID: 28073357
DOI: 10.1186/s12711-016-0275-0

[…] the adipose tissue). to obtain a more reliable set of expressed lncrnas, we took advantage of the large number of replicates to remove genes with low signals. rau et al. [] developed an r package (htsfilter) for rna-seq data analysis to correctly filter out lowly-expressed genes and thereby increase the power of detection in the context of the differential expression of protein-coding genes. […]

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HTSFilter institution(s)
INRA, UMR, Génétique animale et biologie intégrative, Jouy-en-Josas, France; AgroParisTech, UMR1313 Génétique animale et biologie intégrative, Paris, France; Inria Saclay - Île-de-France, Orsay, France
HTSFilter funding source(s)
This work was supported by the French National Research Agency [ANR-09-GENM-006, Biocart project].

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