Welcome @fengtong2018
I’m not sure which public server you are working at – but you could also work at the UseGalaxy servers!
Example tool choices, links are for UseGalaxy.org, but UseGalaxy.eu and UseGalaxy.org.au also host these. Search the tool panel with the tool name to find these.
- RSeQC’s FPKM Count calculates raw read count, FPM, and FPKM for each (link)
- Cufflinks transcript assembly and FPKM (RPKM) estimates for RNA-Seq data (link)
- Then, for count data → Search the panel for Featurecounts or HTSeq-count, then Limma, EdgeR, DESeq2 and other Bioconductor tools like Salmon (TMP counts).
Related protocols are available at our training site, plus many publications and online guides exist. Getting your read data and reference files organized is the important difference compared to using the tools directly. The data files are the “same” – but Galaxy layers in some extra metadata.
GTN Tutorials
- Transcriptomics / Tutorial List
- Learning Pathway: Introduction to Galaxy and Sequence analysis (as a reference for upstream steps)
- FAQ: Extended Help for Differential Expression Analysis Tools (technical help)
- Also see prior Q&A at this forum. Search with the tool name or datatype format and please ask if anything is not clear.
You are welcome to create an account at each of the UseGalaxy serves. Each host extended quota options and the jobs run on large distributed academic clusters.
- More about storage and computational resources.
- How to transfer data between Galaxy servers by URL.
I hope this helps and follow up questions are welcome! 
You could share the URL of the specific server you are working at and we might be able help to get you in contact with the administrators for the request. You can also check for a contact included in the confirmation email you used when originally creating your account (the one with the link). The server may also have contact information included in our directory of known servers here. → https://galaxyproject.org/use/.
And, I didn’t find the exact tools you referenced in our Main ToolShed (an “app store” of tools wrapped for Galaxy) but if you can find the examples and share a link back that would help. We can also make requests for new tool wrappers if you can provide a link to the original development repository or a publication that references it. We can review to see if it appropriate! Tools must be open source and hosted in certain shared environments and I can help to check and make the request.
That’s a lot of information! Your question is a good one for people newer to Galaxy, so I thought an extended reply might help you now, then others later on who find this topic. 