RNA-seq data were analyzed using 5 different quantification strategies
and 2 different transcriptome annotations, for 10 total analyses.

## Data exploration and QC reports

- [`hisat2_grch38_snp_tran_ensembl.85-exploration.html`](hisat2_grch38_snp_tran_ensembl.85-exploration.html)
- [`hisat2_grch38_snp_tran_knownGene-exploration.html`](hisat2_grch38_snp_tran_knownGene-exploration.html)
- [`kallisto_hg38.analysisSet_ensembl.85-exploration.html`](kallisto_hg38.analysisSet_ensembl.85-exploration.html)
- [`kallisto_hg38.analysisSet_knownGene-exploration.html`](kallisto_hg38.analysisSet_knownGene-exploration.html)
- [`salmon_hg38.analysisSet_ensembl.85-exploration.html`](salmon_hg38.analysisSet_ensembl.85-exploration.html)
- [`salmon_hg38.analysisSet_knownGene-exploration.html`](salmon_hg38.analysisSet_knownGene-exploration.html)
- [`shoal_hg38.analysisSet_ensembl.85-exploration.html`](shoal_hg38.analysisSet_ensembl.85-exploration.html)
- [`shoal_hg38.analysisSet_knownGene-exploration.html`](shoal_hg38.analysisSet_knownGene-exploration.html)
- [`star_hg38.analysisSet_ensembl.85-exploration.html`](star_hg38.analysisSet_ensembl.85-exploration.html)
- [`star_hg38.analysisSet_knownGene-exploration.html`](star_hg38.analysisSet_knownGene-exploration.html)

## Differential expression reports

- [`hisat2_grch38_snp_tran_ensembl.85-diffexp.html`](hisat2_grch38_snp_tran_ensembl.85-diffexp.html)
- [`hisat2_grch38_snp_tran_knownGene-diffexp.html`](hisat2_grch38_snp_tran_knownGene-diffexp.html)
- [`kallisto_hg38.analysisSet_ensembl.85-diffexp.html`](kallisto_hg38.analysisSet_ensembl.85-diffexp.html)
- [`kallisto_hg38.analysisSet_knownGene-diffexp.html`](kallisto_hg38.analysisSet_knownGene-diffexp.html)
- [`salmon_hg38.analysisSet_ensembl.85-diffexp.html`](salmon_hg38.analysisSet_ensembl.85-diffexp.html)
- [`salmon_hg38.analysisSet_knownGene-diffexp.html`](salmon_hg38.analysisSet_knownGene-diffexp.html)
- [`shoal_hg38.analysisSet_ensembl.85-diffexp.html`](shoal_hg38.analysisSet_ensembl.85-diffexp.html)
- [`shoal_hg38.analysisSet_knownGene-diffexp.html`](shoal_hg38.analysisSet_knownGene-diffexp.html)
- [`star_hg38.analysisSet_ensembl.85-diffexp.html`](star_hg38.analysisSet_ensembl.85-diffexp.html)
- [`star_hg38.analysisSet_knownGene-diffexp.html`](star_hg38.analysisSet_knownGene-diffexp.html)

## Comparison between quantification strategies

- [`rnaseq-compare.html`](rnaseq-compare.html)