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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




No version available



  • person_outline Andrea Rau

Publication for HTSFilter

HTSFilter citations


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
call_split See protocol

[…] 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 change >1 […]


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
call_split See protocol

[…] eCounts (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 was perfo […]


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
call_split See protocol

[…] 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 out using […]


Long noncoding RNA repertoire in chicken liver and adipose tissue

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

[…] in 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. Un […]


Niche WNT5A regulates the actin cytoskeleton during regeneration of hematopoietic stem cells

PMCID: 5206491
PMID: 27998927
DOI: 10.1084/jem.20151414

[…] rotocol and niche cell data were generated using UMI-seq, as described previously (). To remove noise from lowly expressed genes, count datasets were subjected to data-driven gene filtering using the HTSFilter R package (; Tables S3 and S5). […]


Enhanced in planta Fitness through Adaptive Mutations in EfpR, a Dual Regulator of Virulence and Metabolic Functions in the Plant Pathogen Ralstonia solanacearum

PLoS Pathog
PMCID: 5135139
PMID: 27911943
DOI: 10.1371/journal.ppat.1006044

[…] iguous matches (same best score for several read-pairs) were removed. Finally, between 8.2 and 23.4M non ambiguous read-pairs were obtained. Mapped reads were imported into R environment. The package HTSFilter was used to eliminate very low-expressed genes from the analysis. A total of 5157 out the predicted 5307 genes were thus kept in. R package DESeq2 was used to normalize and complete the diff […]

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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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