BioInformatics, Software

Question

[hashim.rana11]

Are there any websites or links accessible for acquiring knowledge about Bioinformatics Software?

[barslmn]

https://bio.tools/ is a great website indexing software used in bioinformatics.

[hashim.rana11]

Thank you so much...

[LauferVA]

biostars.org is a great website for that

[Pierre Lindenbaum]

This is just too broad. what did you find so far ?

Answer 1

[colindaven]

https://training.galaxyproject.org/

Answer 2

[Decimus Maximus]

Galaxy is very common but you cannot cluster data in Galaxy (i.e. Seurat or SC3 for clustering and dimensionality reduction), so you may have to download your data and do these analyses using other tools. Visualisation is also an issue in Galaxy as it doesn't have many options for this - not as many as you would have with R or Python, but you can still visualize quality control metrics and differential expression results ( to display graph go to "Graph/Display Data", select the appropriate graphing e.g. bar chart, and upload data and set the parameters as required.

Good luck

Answer 3

[Jesse]

Here's a couple that are geared toward hands-on bioinformatics learning:

• rosalind.info
• sandbox.bio

Answer 4

[rfran010]

There have been some good suggestions, but it seems like you may be asking one of two questions, either (1) how to do bioinformatics? or (2) you have a basic understanding of how to work with bioinformatic tools, but are looking for good tools to use.

Personally, I think the answer to either question is the same: Come up with a specific task you want to do. If you are a complete beginner, maybe this is "analyze RNA-seq data", or if you have some know-how, maybe it is "tools to call peaks or tools to align long read data"

Then ask again and google with a clearer goal in mind. One problem I can see with trying to find tools by looking at a list is that you won't necessarily know the advantages and disadvantages of those tools, the contexts they are most useful in, or if they are commonly used in the field.

Additional places to look include manuscript methods and published pipelines, even if you don't have a need for the pipeline itself, the authors often have compiled useful tools and scripts that can accomplish specific tasks or at least help you figure out how to write your own custom script.

If you are a beginner, then I think it is easiest to start by figuring out the steps necessary for a specific type of bioinformatic analysis. So maybe just focus on RNA-seq analysis. Then learn the steps and how to accomplish each step and the important considerations for that step. Then, you could ask a more specific question that could lead to more helpful answers.

There are plenty of free resources online, but biostars also has a nice compilation of bioinformatic knowledge in their manual (for a nominal fee).