DOI: 10.5061/dryad.8pk0p2nnd
title: Extended data tables to Haering and Habermann, F1000Res, RNfuzzyApp: an R shiny RNA-seq data analysis app for visualisation, differential expression analysis, time-series clustering and enrichment analysis

description: Background  RNA-seq is a widely adopted affordable method for
 large scale gene expression profiling. However, user-friendly and
 versatile tools for wet-lab biologists to analyse RNA-seq data beyond
 standard analyses such as differential expression, are rare. Especially,
 the analysis of time-series data is difficult for wet-lab biologists
 lacking advanced computational training. Furthermore, most meta-analysis
 tools are tailored for model organisms and not easily adaptable to other
 species. Results With RNfuzzyApp, we provide a user-friendly, web-based
 R-shiny app for differential expression analysis, as well as time-series
 analysis of RNA-seq data. RNfuzzyApp offers several methods for
 normalization and differential expression analysis of RNA-seq data,
 providing easy-to-use toolboxes, interactive plots and downloadable
 results. For time-series analysis, RNfuzzyApp presents the first
 web-based, automated pipeline for soft clustering with the Mfuzz R
 package, including methods to aid in cluster number selection, Mfuzz loop
 computations, cluster overlap analysis, as well as cluster enrichments.
 Conclusion RNfuzzyApp is an intuitive, easy to use and interactive R shiny
 app for RNA-seq differential expression and time-series analysis, offering
 a rich selection of interactive plots, providing a quick overview of raw
 data and generating rapid analysis results. Furthermore, its orthology
 assignment, enrichment analysis, as well as ID conversion functions are
 accessible to non-model organisms.
description: Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt: mean
 values calculated from raw reads of replicates, downloaded from gene
 expression omnibus (dataset GSE143430
 https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE143430).
 <br>
 Haering_etal_extendedDatatable_1a_Tabulamurissenis_3vs12m_DEA.txt: Tabula
 muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_1b_Tabulamurissenis_3vs27m_DEA.txt: Tabula
 muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_1c_Tabulamurissenis_12vs27m_DEA.txt: Tabula
 muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_1d_Tabulamurissenis_3vs12m_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_1e_Tabulamurissenis_3vs27m_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_1f_Tabulamurissenis_12vs27m_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_2a_Tabulamurissenis_cluster1_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_2b_Tabulamurissenis_cluster2_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_2c_Tabulamurissenis_cluster3_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_2d_Tabulamurissenis_cluster4_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_2e_Tabulamurissenis_cluster5_gpofiler.txt:
 Tabula muris senis limb muscle data
 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE132040) from 3, 12
 and 27month males, processed with RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3a_DmLeg_cluster1_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3b_DmLeg_cluster2_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3c_DmLeg_cluster3_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3d_DmLeg_cluster4_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3e_DmLeg_cluster5_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3f_DmLeg_cluster6_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3g_DmLeg_cluster7_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3h_DmLeg_cluster8_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3i_DmLeg_cluster9_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3j_DmLeg_cluster10_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3k_DmLeg_cluster11_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
 <br>
 Haering_etal_extendedDatatable_3l_DmLeg_cluster12_gpofiler.txt:
 Haering_etal_extendedData_DmdevLeg_GSE143430_mean.txt processed with
 RNfuzzyApp
 (https://gitlab.com/habermann_lab/rna-seq-analysis-app)
description: Details on data processing and analysis can be found in the
 associated article.