RNA-Seq

Kallisto / Sleuth

ftp://ftp.ncbi.nih.gov/refseq/H_sapiens/RefSeqGene/

https://www.bioconductor.org/help/workflows/rnaseqGene/

Alignment to transcript index with kallisto or salmon and analysis with something like sleuth, edgeR or DESeq2.

Or alignment to index created from full human genome and gene feature file with something like STAR, counts extracted with something like featureCounts and analysis again with something like DESeq2.

http://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.html

https://digibio.blogspot.com/2017/11/rna-seq-analysis-hisat2-featurecounts.html