Try omicX (https://omictools.com/transcriptomics-category)

Can recommend usegalaxy.org. A user-friendly UI for lots of packages used for transcriptome analysis. There are a lot of tutorials and walkthroughs for each package if you google transcriptome + Galaxy.

As recommended by Norman van Rhijn , usegalaxy.org is very user-friendly and intuitive.

Here is the pipeline you can follow if you are using RNA seq data:

1. Get data (Upload your dataset, a reference genome of your organism of interest and its annotation file (GFF or GTF)

2. FastQC (for quality check of your data)

3. If required, use trimmomatic ( for adapter and removal )

4. HISAT2 for reads alignment (using reference genome and your dataset)

5. FeatureCounts for reads quantification (using BAM file generated from HISAT2 and GFF/GTF annotation file)

6. From here you can either go for differential expression analysis or any other analysis.

7. For differential expression analysis, you can either use DEseq2 or edgeR.

( All these tools with information on their usage are available on usegalaxy UI).

For how to use, here is the link: https://training.galaxyproject.org/training-material/topics/introduction/tutorials/galaxy-intro-short/tutorial.html

thanks all of you