Field-wide assessment of differential HT-seq from NCBI GEO database

<p>We analysed the field of&nbsp;expression profiling by high throughput sequencing,&nbsp;or HT-seq, in terms of replicability and reproducibility, using data from the NCBI GEO (Gene Expression Omnibus) repository.&nbsp;</p> <p>&nbsp;</p> <p>- This release includes GEO series published up to Dec-31, 2020;</p> <p>&nbsp;</p> <p><a href="https://zenodo.org/api/files/320af641-0181-4e73-adfa-d2d2e61dbf23/geo-htseq.tar.gz?versionId=852d4e0b-3c5b-4156-ac80-9b27cc1e53cb">geo-htseq.tar.gz&nbsp; </a>archive contains following files:</p> <p>- output/parsed_suppfiles.csv,&nbsp;p-value histograms, histogram classes, estimated number of true null hypotheses (pi0).</p> <p>- output/document_summaries.csv,&nbsp;document summaries of NCBI GEO series.</p> <p>- output/suppfilenames.txt, list of all supplementary file names of NCBI GEO submissions.</p> <p>- output/suppfilenames_filtered.txt, list of supplementary file&nbsp;names used for downloading files from NCBI GEO.</p> <p>-&nbsp;output/publications.csv, publication info of NCBI GEO series.</p> <p>- output/scopus_citedbycount.csv, Scopus citation info of NCBI GEO series</p> <p>- output/spots.csv, NCBI SRA sequencing run metadata.</p> <p>- output/cancer.csv, cancer related experiment accessions.</p> <p>- output/transcription_factor.csv, TF related experiment accessions.</p> <p>- output/single-cell.csv, single cell experiment accessions.</p> <p>- blacklist.txt, list of&nbsp;supplementary files&nbsp;that were either too large to import or were causing computing environment crash during import.</p> <p>&nbsp;</p> <p>Workflow to produce this dataset is available on Github at&nbsp;<a href="https://github.com/rstats-tartu/geo-htseq">rstats-tartu/geo-htseq</a>.</p> <p>&nbsp;</p> <p><a href="https://zenodo.org/api/files/320af641-0181-4e73-adfa-d2d2e61dbf23/geo-htseq-updates.tar.gz">geo-htseq-updates.tar.gz </a>archive contains files:</p> <p>- results/detools_from_pmc.csv, differential expression analysis programs inferred from published articles</p> <p>- results/n_data.csv, manually curated sample size info for NCBI GEO HT-seq series</p> <p>- results/simres_df_parsed.csv, pi0 values estimated from differential expression results obtained from simulated RNA-seq data</p> <p>- results/data/parsed_suppfiles_rerun.csv, pi0 values estimated using smoother method from anti-conservative p-value sets</p> <p>&nbsp;</p> <p>&nbsp;</p>