I have tried javaTreeview tools its really handy to view heatmap along with the clustering it forms .But this seem to be quite old not being updated .Are there any other tool similar to JavaTreeview ?Do suggest
3 answers
Never saw a better alternative GUI to JavaTreeview in terms of searching and selecting subset of genes and playing around.
For plotting, I use ComplexHeatmap which allows many customisations.
Yes. There is no easy tool to search the genes like in javaTreeView. But complex heatmap provides lot of customizations to make nice heatmaps and to annotate them. It takes a while to get used to it.
If you are interested in a Java library only for heatmap visualization, then you can have a look at GC4S (https://github.com/hlfernandez/GC4S/), which includes a JHeatMap component to create interactive, customizable heatmaps. For heatmap and dendogram visualization, I also think that JavaTreeview is a very good option.
Many of the R heatmap packages provide similar functions.
Log in to answer this question.
-
Any tools like IPRStats but newer?
written by zack.saud •
-
Visualizing a set of genes in ENCODE ChIPseq dataset-Any tools or tutorials?
written by goodwinjinesh •
-
vContact2 donwload and command line
written by vishalchanda364 •
-
miRPara for novel miRNA discovery
written by Rituriya •
-
extract dendrogram cluster from pheatmap
written by 1769mkc
-
comparative genomic analysis to obtain current status of each fungal genome existing databases and …
written by shivkumar4589 •
-
How to do unsupervised clustering using copy number variation data?
written by dr.chenway •
-
DNA sequence clustering tools
written by ngs101.com
-
Finding Similar Genomic Regions
written by Brett
-
Simple Tool For Finding Known Regulatory Motifs In A Single (Eukaryotic) Sequence
written by Eric Fournier
A software being old and not updated is not necessarily a bad thing especially if it is still being used. It could mean the tool is stable, no new bugs are found and there are no need for new functionality. It's often a pain when tools are updated too often.
It is being updated, in fact: http://treeview.princeton.edu. We're on the cusp of the first beta release. Final code review in process. Prepping publication too.
Honestly, I liked the previous version. It looks very complicated now.
wow...after 9 months of my query i see the new one..cool will give it a try
rleach : Please make an official announcement when ready.
@rleach I guess i can give it a try it won;t be an issue i suppose..