LRpath protocols

View LRpath computational protocol

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LRpath specifications

Information


Unique identifier OMICS_04057
Name LRpath
Interface Web user interface
Restrictions to use None
Computer skills Basic
Stability Stable
Maintained Yes

Subtool


  • RNA-Enrich

Documentation


Maintainer


  • person_outline Snehal Patil <>

Information


Unique identifier OMICS_04057
Name LRpath
Software type Package/Module
Interface Command line interface
Restrictions to use None
Operating system Unix/Linux, Mac OS, Windows
Programming languages R
Computer skills Advanced
Stability Stable
Maintained Yes

Subtool


  • RNA-Enrich

Versioning


Add your version

Documentation


Maintainer


  • person_outline Snehal Patil <>

Publications for LRpath

LRpath in pipelines

 (2)
2018
PMCID: 5816015
PMID: 29453456
DOI: 10.1038/s41467-018-03019-z

[…] using the negative binomial statistical model of read counts as implemented in the edger bioconductor package. the kegg pathways and msigdb gene sets enrichment analysis was performed using lrpath methodology as implemented in the clean package, and ranked by the enrichment p-value. functional enrichment analysis of the genes that are both downregulated in mir-128oe hearts […]

2016
PMCID: 4853320
PMID: 26946493
DOI: 10.1007/s13238-015-0241-6

[…] expressed genes between two groups were identified by two-group comparison using intensity-based empirical bayes method (ibmt) (sartor et al., ). pathway enrichment analysis was performed using the lrpath methodology (sartor et al., ) implemented in the clean package (freudenberg et al., )., qrt-pcr was performed using a dna engine opticon2 real-time pcr detection system (mj research) and sybr […]


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LRpath in publications

 (25)
PMCID: 5816015
PMID: 29453456
DOI: 10.1038/s41467-018-03019-z

[…] using the negative binomial statistical model of read counts as implemented in the edger bioconductor package. the kegg pathways and msigdb gene sets enrichment analysis was performed using lrpath methodology as implemented in the clean package, and ranked by the enrichment p-value. functional enrichment analysis of the genes that are both downregulated in mir-128oe hearts […]

PMCID: 5534072
PMID: 28754123
DOI: 10.1186/s13073-017-0458-5

[…] hierarchical clustering of normalized gene expression data was done in r with the hclust command (method = “ward”, distance = “euclidean”), pathway analysis was conducted using the web-based tool lrpath [] using all gene ontology (go) term annotations, adjusting to gene read count with rna-enrich, including directionality and limiting maximum go term size to 500 genes. go term visualization […]

PMCID: 5499851
PMID: 28369632
DOI: 10.1093/nar/gkx204

[…] continuous predictor variable in de analysis., several lines of evidence support the biological validity of the genes detected by macau. first, we performed gene ontology (go) analysis using lrpath () on t2d and gl associated genes identified by macau, as in the fusion study () (). the go analysis results for t2d and gl are consistent with previous studies (,) and are also similar […]

PMCID: 5298317
PMID: 28178311
DOI: 10.1371/journal.pone.0171694

[…] transcriptionally predictive methylation-driven genes and pathways in twelve different cancers. alternatively, kim et al. proposed a logistic regression-based method for gene set enrichment, termed lrpath [], for the investigation of important methylation-driven pathways. moreover, pathway similarities across different types of cancers are included in this analysis., in numerous studies, […]

PMCID: 5351587
PMID: 28008156
DOI: 10.18632/oncotarget.14050

[…] between the four groups. fdr was controlled using the benjamini-hochberg method []., gene ids, p-values and fold changes from rna-seq differential expression analyses were used as input in lrpath [, ] to perform gene set enrichment testing. we tested go terms and kegg pathways with the directional test option, which identifies gene sets enriched with up-regulated or down-regulated […]


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LRpath institution(s)
Center for Computational Medicine and Biology, University of Michigan, Ann Arbor, MI, USA

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