GEO2R software 'BART' not working? and is there any good interactive volcano plot library?

I was looking over some microarray data analysis tools and found 'BART' which is a free software where you can do the same thing as GEO2R in ncbi-geo.

This is the website for BART

However, the server seemed to be disconnected... are they still providing service?

Also, is there a good interactive volcano plot library?

Currently I managed to draw a volcanoplot with volcanoplot() from umap.

• 1,064 views • link

updated 5.5 years ago by Kevin Blighe

• written 5.5 years ago by orzrzlyo •

1 answer

For the issue with BART, please contact the developers of that app - here is the publication: https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-018-2308-x

For another interactive volcano plot, please try https://huygens.science.uva.nl/VolcaNoseR/

Kevin

• 0 views • link

written 5.5 years ago by Kevin Blighe

More posts like this

Tool: Update: Jetomics v2.0 – Now with Local FASTQ Pipelines, Xenium Spatial Support, and Free Acad…
written 1 month ago by Aram Donyaee •

Hi everyone, About four months ago, I posted here about Jetomics, our private, local desktop platform for analyzing transcriptomics data. We received some incredibly constructive …
GEO dataset Microarray data analysis help
written 2.7 years ago by Confused_human •

Hello Everyone , I am new to microarray dataset . I want to do this similar kind of plotting using this same mentioned dataset for …
Tutorial: GEO Data Mining (II) - Differential gene expression analysis and visualization with compl…
written 3.6 years ago by Novogene •

In the previous two articles, "[Gene Expression Omnibus Data Mining (IA) – Quick and Easy Download of GEO Data][1]" and "[GEO Data Mining (IB) - …
Forum: Build a Visual Analytic App for Rna-seq data [Ideas Accepted]
written 4.0 years ago by ali •

Hi everyone , I will have to work on an exam and the topic is to build a Visual Analytic Application about any dataset we …
Absence of significant values in the analyzes with GEO2R
written 5.7 years ago by RafaelMP

Hi! I intend to use different array experiments, stored in GEO, to conduct a reanalysis. As a starting point, I used the GEO2R code, but …
Reviewing some of these answers from bioinformatics lab
written 5.9 years ago by Voyboy488 •

Just college student taking upper division lab in bioinformatics, not sure if its okay to post questions like this on this forum, if not then …
Error in function (type, msg, asError = TRUE); unable to analyze HTA2.0 GSE set
written 8.9 years ago by collinmlanger •

Hello everyone, I'm fairly new to analyzing micro-arrays, but that being said, GSE103974 in particular is giving me some problems. I've tried various analysis pipelines …
Weird Kmer at 5' of read 1 in paired-end RNA-seq
written 9.3 years ago by izzy.yichao.cai

Hi all, I've come across a weird issue with my RNA-seq data. Some details about the data: There 4 libraries of RNA, all total RNA-seq …
Help with finding tutors for GO enrichment analysis, R, Cytoscape, Python, Linux, Perl, Octave and/…
written 11.5 years ago by david.ballester •

I forward this message, may be someone could give a hand? From: Student at University of Arkansas at Little Rock Hi, I am a visually …
Creating a log intensity plot of normalized microarrays
written 11.7 years ago by StatsBio •

I'm currently working on a microarray dataset from NIH's Gene Expression Omnibus using R. I was wondering how to plot a log intensity/density plot on …