Research graph
References from ARMT: An automatic RNA-seq data mining tool based on comprehensive and integrative analysis in cancer research. Local targets link to admitted publications; unresolved targets remain external evidence.
Cancer RNA-Seq Nexus: a database of phenotype-specific transcriptome profiling in cancer cells
10.1093/nar/gkv1282 · 2016 · External reference
10.1038/cr.2012.30
10.1038/cr.2012.30 · External reference
10.1016/j.ygyno.2018.10.002
10.1016/j.ygyno.2018.10.002 · External reference
NCBI GEO: archive for functional genomics data sets-update
10.1093/nar/gks1193 · 2013 · External reference
10.1093/nar/gky964
10.1093/nar/gky964 · External reference
10.1172/jci127046
10.1172/jci127046 · External reference
Pan-cancer characterization of immune-related lncRNAs identifies potential oncogenic biomarkers
2020 · External reference
10.1038/s41586-020-1970-0
10.1038/s41586-020-1970-0 · External reference
10.1016/j.cell.2019.01.025
10.1016/j.cell.2019.01.025 · External reference
A survey of best practices for RNA-seq data analysis
2016 · External reference
A genome-wide transcriptomic analysis of protein-coding genes in human blood cells
10.1126/science.aax9198 · 2019 · External reference
Characterization of glycolysis-associated molecules in the tumor microenvironment revealed by pan-cancer tissues and lung cancer single cell data
2020 · External reference
10.1007/s10142-018-0636-6
10.1007/s10142-018-0636-6 · External reference
Integrated analysis of key differentially expressed genes identifies DBN1 as a predictive marker of response to endocrine therapy in luminal breast cancer
10.3390/cancers12061549 · 2020 · External reference
Screening and identification of key biomarkers for retinoblastoma Evidence from bioinformatics analysis
2020 · External reference
Application of NanoString technologies in angioimmunoblastic T cell lymphoma
10.1007/s13258-020-00919-7 · 2020 · External reference
10.1093/bioinformatics/btp616
10.1093/bioinformatics/btp616 · External reference
10.1186/s13059-014-0550-8
10.1186/s13059-014-0550-8 · External reference
10.1093/nar/gkv007
10.1093/nar/gkv007 · External reference
10.1177/0962280211428386
10.1177/0962280211428386 · External reference
10.1038/nprot.2012.016
10.1038/nprot.2012.016 · External reference
10.1038/nbt.2450
10.1038/nbt.2450 · External reference
baySeq: Empirical Bayesian methods for identifying differential expression in sequence count data. Bmc
2010 · External reference
10.1038/nmeth.4324
10.1038/nmeth.4324 · External reference
GCSscore: an R package for differential gene expression analysis in Affymetrix/Thermo-Fisher whole transcriptome microarrays. Bmc
2021 · External reference
ideal: an R/Bioconductor package for interactive differential expression analysis. Bmc
10.1101/2020.01.10.901652 · 2020 · External reference
INDEED: R package for network based differential expression analysis
2018 · External reference
Comparison of software packages for detecting differential expression in RNA-seq studies
10.1093/bib/bbt086 · 2015 · External reference
Empirical assessment of analysis workflows for differential expression analysis of human samples using RNA-Seq. Bmc
2017 · External reference
New functionalities in the TCGAbiolinks package for the study and integration of cancer data from GDC and GTEx
10.1371/journal.pcbi.1006701 · 2019 · External reference
Identification of tumor immune infiltration-associated lncRNAs for improving prognosis and immunotherapy response of patients with non-small cell lung cancer
2020 · External reference
Risk factors associated with mortality among patients with COVID-19 in intensive care units in Lombardy, Italy
10.1001/jamainternmed.2020.3539 · 2020 · External reference
10.1016/j.celrep.2018.03.077
10.1016/j.celrep.2018.03.077 · External reference
Comparison of GENCODE and RefSeq gene annotation and the impact of reference geneset on variant effect prediction
10.1186/1471-2164-16-s8-s2 · 2015 · External reference
10.1111/j.1748-1716.2011.02293.x
10.1111/j.1748-1716.2011.02293.x · External reference
Ten years of pathway analysis: current approaches and outstanding challenges
10.1371/journal.pcbi.1002375 · 2012 · External reference
Analyzing gene expression data in terms of gene sets: methodological issues
10.1093/bioinformatics/btm051 · 2007 · External reference
ToPASeq: an R package for topology-based pathway analysis of microarray and RNA-Seq data. Bmc
2015 · External reference
Network enrichment analysis: extension of gene-set enrichment analysis to gene networks
10.1186/1471-2105-13-226 · 2012 · External reference
10.1093/bioinformatics/bts389
10.1093/bioinformatics/bts389 · External reference
10.1093/nar/gkh036
10.1093/nar/gkh036 · External reference
10.1093/nar/gkt1076
10.1093/nar/gkt1076 · External reference
10.1073/pnas.0506580102
10.1073/pnas.0506580102 · External reference
10.1177/0962280212460441
10.1177/0962280212460441 · External reference
GSVA: gene set variation analysis for microarray and RNA-Seq data
10.1186/1471-2105-14-7 · 2013 · External reference
10.1038/s41586-020-2099-x
10.1038/s41586-020-2099-x · External reference
10.1038/s41586-020-2969-2
10.1038/s41586-020-2969-2 · External reference
10.1016/j.cell.2020.05.007
10.1016/j.cell.2020.05.007 · External reference
10.1016/j.cell.2020.11.042
10.1016/j.cell.2020.11.042 · External reference
10.1038/s41586-019-1576-6
10.1038/s41586-019-1576-6 · External reference
Metascape provides a biologist-oriented resource for the analysis of systems-level datasets
2019 · External reference
10.1101/gr.239244.118
10.1101/gr.239244.118 · External reference
TCGAbiolinks: an R/Bioconductor package for integrative analysis of TCGA data
10.1093/nar/gkv1507 · 2016 · External reference
10.1002/jcb.28927
10.1002/jcb.28927 · External reference
Integrated Analysis of MicroRNA (miRNA) and mRNA Profiles reveals reduced correlation between microrna and target gene in cancer
2018 · External reference
Integrative analysis reveals comprehensive altered metabolic genes linking with tumor epigenetics modification in pan-cancer
2019 · External reference
B-cell lymphoma 2 family genes show a molecular pattern of spatiotemporal heterogeneity in gynaecologic and breast cancer
2020 · External reference
Identification and validation of circulating MicroRNA signatures for breast cancer early detection based on large scale tissue-derived data
10.4048/jbc.2018.21.e56 · 2018 · External reference
KnowSeq R-Bioc package: The automatic smart gene expression tool for retrieving relevant biological knowledge
10.1016/j.compbiomed.2021.104387 · 2021 · External reference
RNASEQR-a streamlined and accurate RNA-seq sequence analysis program
2012 · External reference
RTCGAToolbox: A new tool for exporting TCGA firehose data
10.1371/journal.pone.0106397 · 2014 · External reference
From RNA-seq reads to differential expression results
10.1186/gb-2010-11-12-220 · 2010 · External reference
10.1089/omi.2011.0118
10.1089/omi.2011.0118 · External reference
10.1038/s41588-018-0318-2
10.1038/s41588-018-0318-2 · External reference
10.1101/gad.259796.115
10.1101/gad.259796.115 · External reference
10.1111/pcmr.12661
10.1111/pcmr.12661 · External reference
10.1016/j.tcb.2017.10.006
10.1016/j.tcb.2017.10.006 · External reference
10.1093/bib/bby023
10.1093/bib/bby023 · External reference
