Changes in version 2.25.6 Other changes - The progress messages of the values/ranks methods name each experiment instead of STRING's job, e.g. Experiment logFC: 599 enriched terms: a column of the table, or, for a vector, the values as given (e.g. mapped$logFC). With a table, each experiment gets a message when it finishes or fails. The job id is still given when a job is submitted, and in the messages that say how to get results later. Changes in version 2.25.5 Other changes - Vignette: the GSEA code is plain code in the vignette's R script (it was commented out there), so it can be run, e.g. in RStudio. It runs only in an interactive R session, not while the vignette is built. Changes in version 2.25.4 New features - get_values_ranks_enrichment(): a GSEA-like enrichment analysis of a ranked list of proteins, computed on STRING's servers (STRING's values/ranks enrichment; STRING 12.0 or later). The results have the columns of get_enrichment() where they mean the same; STRING's statistics differ from those of fgsea or clusterProfiler. The values can also be given alone, as a named vector. - Many experiments at once: with a table of values, each experiment becomes a job, run side by side on STRING's servers (up to 1000 jobs per API key). For many experiments, e.g. tens or hundreds of columns, submit_values_ranks_enrichment() submits them without blocking the R session; get_values_ranks_status() and get_values_ranks_results() follow them and collect the results later, also in a new R session. - get_api_key(): the values/ranks methods use one API key per computer, which the package requests and saves; STRINGDB_API_KEY is used instead when it is set. - get_enrichment(add_scores = TRUE) adds STRING's strength and signal columns (STRING 12.5). - get_enrichment_figure(): the categories GWAS and Hallmark, the palette "red_blue", and "count" for x_axis and sort_by (STRING 12.5). - get_png(), get_link() and plot_network(): channels selects the evidence channels (STRING 12.0 or later), and add_color_nodes and add_white_nodes add interaction partners. Bug fixes - A download cut off part-way no longer leaves a partial file in the download cache; delete such a file left by an older version to download it again. - Downloads of STRING files may take up to 300 seconds instead of R's default 60. - map()'s note about unmapped identifiers ends with a line break. Other changes - Depends on R 4.0.0 or later (for tools::R_user_dir()). - The package sends its caller identity, "STRINGdb-package", with every request to STRING. The caller_identity argument of get_png(), get_link(), get_enrichment_figure() and get_geneset_description() is ignored, with a warning. - New arguments can make abbreviated argument names ambiguous, e.g. show = in get_link() and plot_network(): use the full names. - igraph's deprecated function names are replaced by their current names. - The unit tests that call STRING are deactivated when STRING cannot be reached. Planned for the next Bioconductor release - inputGenes and preferredNames of get_enrichment() and get_values_ranks_enrichment() will become list columns instead of comma-separated text (code that splits them with strsplit() will need to change). - The caller_identity argument will be removed. Changes in version 2.25.3 Bug fixes - STRINGdb$new() creates an object for a known STRING version (11.0, 11.0b, 11.5, 12.0 and 12.5) without any request to STRING, so it also works offline or when string-db.org cannot be reached. Without a version, STRING is asked for its current version with a timeout, and the newest known version is used, with a warning, when STRING cannot be reached. An unavailable version now stops with an error that names the available versions. - map() no longer gives wrong results in three cases: missing (NA) or empty identifiers were mapped to a real protein (for human, every row without a gene name got 9606.ENSP00000222345); with several identifier columns, the identifiers no longer matched the rest of their rows; and with takeFirst = FALSE or usePreferredSources = FALSE some identifiers came back upper-cased. Aliases containing characters such as the hyphen U+2010 can now be mapped, and get_aliases() includes them. The identifier columns keep their type (e.g. integer Entrez ids are no longer turned into text), and with several identifier columns the rows keep their input order. - get_summary(string_ids) works without required_score, as documented. - post_payload() with logo_imgF or legend_imgF works again. Changes in version 2.25.2 - get_png() and get_enrichment_figure() stop with STRING's explanation when STRING refuses the request, for example a PNG of more than 150,000 interactions, instead of returning STRING's error answer as the picture. - Requests that STRING's servers answer with an error (HTTP 5xx, e.g. a gateway timeout) stop with the status code instead of returning the error page as data. - New options for STRING 12.5 (older versions do not use them, with a warning): - get_enrichment() and get_enrichment_figure(): max_fdr, min_gene_count, min_strength, min_signal and merge_similarity filter the terms as the enrichment table of the STRING website; - get_enrichment_figure(): graph_type ("dotplot" or "barplot") and sort_by; - get_png(): clustering of the network picture (network_clustering_algorithm "kmeans", "mcl" or "leiden", and its options), as the Clusters tab of the STRING website. Changes in version 2.25.1 - Support for STRING 12.5, including its directed regulatory network (network_type = "regulatory"). - New method get_geneset_description(), and more options for network pictures and links.