tximport protocols

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tximport specifications

Information


Unique identifier OMICS_11762
Name tximport
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 3.0
Computer skills Advanced
Version 1.8.0
Stability Stable
Requirements
limma, utils, testthat, edgeR, rmarkdown, knitr, TxDb.Hsapiens.UCSC.hg19.knownGene, tximportData, rhdf5, jsonlite, readr(>=0.2.2), DESeq2(>=1.11.6)
Maintained Yes

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  • person_outline Charlotte Soneson <>

Publication for tximport

tximport in pipelines

 (5)
2018
PMCID: 5952343
PMID: 29580841
DOI: 10.1016/j.ebiom.2018.03.010

[…] then the gene-level estimates, representing the overall transcriptional output of each gene, were obtained by summing the corresponding transcript-level estimates using a bioconductor package, tximport (). differential gene expression analysis was conducted at the gene level using edger, after applying the filter for at least half of the samples above the detection level (cpm > 1), […]

2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] using salmon 0.7.0. rock dove transcripts were mapped to genes from the gallus gallus genome version 5, using blast. all data were then imported into the r statistical package (version 3.3.0) using tximport for gene level evaluation of gene expression, which was calculated using edger (version 3.1.4) following tmm normalization and correction for multiple hypothesis tests by setting the false […]

2017
PMCID: 5394691
PMID: 28417958
DOI: 10.1038/srep45125

[…] to the rock dove reference hpg transcriptome using salmon, which resulted in between 70% and 80% read mapping. these mapping data were imported into r and summarized into gene-level counts using tximport, after which, edger was used to generate normalized estimates of gene expression. patterns of transcript-expression overlap are presented in . of the 15,102 genes expressed in the hpg, 7,529 […]

2017
PMCID: 5614841
PMID: 28805815
DOI: 10.1038/nn.4620

[…] strand-specific single-end rna-seq read files were analyzed to obtain transcript level counts using kallisto, with the settings –rf-stranded -b 100. the counts were subsequently passed to the tximport r package to collapse to gene level counts. pairwise differential expression analysis between groups was then performed using edger with default settings., using an adjusted p-value cutoff […]

2017
PMCID: 5715069
PMID: 29203769
DOI: 10.1038/s41467-017-01963-w

[…] set, as recommended in the cytofkit manual., raw rna-seq reads were pseudoaligned to the mouse transcriptome (ensembl, grcm38 release 79) using kallisto. expression analysis was conducted using the 'tximport' and 'deseq2' r packages adhering to the guidelines suggested in the deseq2 manual, . forty-one erythrocyte-associated transcripts were excluded due to high erythrocyte transcription within […]


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tximport in publications

 (24)
PMCID: 5929421
PMID: 29731978
DOI: 10.18632/oncotarget.24808

[…] differential expression analysis was performed with the kallisto software (v0.42.1)+ [] on the raw fastq files with default parameters, followed by differential expression analysis using the tximport (v1.0.3) [] and edger (v3.14.0)+ [] r packages. all hdegs and degs within the model are presented in . the grch37 human reference genome assembly was used in all steps of the analyses. […]

PMCID: 5896116
PMID: 29650040
DOI: 10.1186/s13059-018-1419-z

[…] methods were compared to standard gene-level differential analysis performed with sleuth and deseq2. sleuth was run in gene mode with 30 bootstraps. deseq2 was run on gene counts obtained using tximport [] to aggregate transcript quantifications, except the case of 3’ quantseq dataset, where gene counts were obtained by summing reads that uniquely map to a gene. both sleuth and deseq2 […]

PMCID: 5896242
PMID: 29634949
DOI: 10.1016/j.ccell.2018.03.003

[…] linear model using a multi-factorial design matrix (tumor stage, dog) and applying a fold-change cut-off of +/- 10 and a benjamini-hochberg adjusted p value cut-off of 0.01., for the 7xx ctvts, tximport was used to import the mapped counts data into r and summarize the transcripts-level data into gene level as described ((). counts for 21047 genes were normalized and further analyzed using […]

PMCID: 5952343
PMID: 29580841
DOI: 10.1016/j.ebiom.2018.03.010

[…] then the gene-level estimates, representing the overall transcriptional output of each gene, were obtained by summing the corresponding transcript-level estimates using a bioconductor package, tximport (). differential gene expression analysis was conducted at the gene level using edger, after applying the filter for at least half of the samples above the detection level (cpm > 1), […]

PMCID: 5873900
PMID: 29432129
DOI: 10.1534/g3.117.300504

[…] cells (). expression analysis was carried out on single end 50bp reads. gene expression levels were quantitated using kallisto (). these data were converted to counts and summarized per gene using tximport (). when comparing genes associated with the two classes, we assigned genes to the nearest peak., all raw and processed data are deposited under accession number gse97413., chip-seq data […]


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tximport institution(s)
Institute for Molecular Life Sciences, University of Zurich, Zurich, Switzerland; SIB Swiss Institute of Bioinformatics, University of Zurich, Zurich, Switzerland; Department of Biostatistics and Computational Biology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Biostatistics, Harvard TH Chan School of Public Health, Boston, MA, USA
tximport funding source(s)
This work was supported by the “RNA & Disease” National Center of Competence in Research, an SNSF project grant (143883) by the European Commission through the 7th Framework Collaborative Project RADIANT (Grant Agreement Number: 305626), and by NIH grant 5T32CA009337-35.

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