{"action":"published","release":{"url":"https://api.github.com/repos/bartongroup/RATS/releases/6587829","assets_url":"https://api.github.com/repos/bartongroup/RATS/releases/6587829/assets","upload_url":"https://uploads.github.com/repos/bartongroup/RATS/releases/6587829/assets{?name,label}","html_url":"https://github.com/bartongroup/RATS/releases/tag/v0.5.0","id":6587829,"tag_name":"v0.5.0","target_commitish":"master","name":"RATs v0.5.0 (R source package)","draft":false,"author":{"login":"fruce-ki","id":18140986,"avatar_url":"https://avatars1.githubusercontent.com/u/18140986?v=3","gravatar_id":"","url":"https://api.github.com/users/fruce-ki","html_url":"https://github.com/fruce-ki","followers_url":"https://api.github.com/users/fruce-ki/followers","following_url":"https://api.github.com/users/fruce-ki/following{/other_user}","gists_url":"https://api.github.com/users/fruce-ki/gists{/gist_id}","starred_url":"https://api.github.com/users/fruce-ki/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/fruce-ki/subscriptions","organizations_url":"https://api.github.com/users/fruce-ki/orgs","repos_url":"https://api.github.com/users/fruce-ki/repos","events_url":"https://api.github.com/users/fruce-ki/events{/privacy}","received_events_url":"https://api.github.com/users/fruce-ki/received_events","type":"User","site_admin":false},"prerelease":false,"created_at":"2017-06-19T16:19:24Z","published_at":"2017-06-19T16:42:07Z","assets":[],"tarball_url":"https://api.github.com/repos/bartongroup/RATS/tarball/v0.5.0","zipball_url":"https://api.github.com/repos/bartongroup/RATS/zipball/v0.5.0","body":"# New features\r\n\r\n1. The `$Transcripts` table records absolute fold-change per transcript (`log2FC`). How meaningful that is will depend on whether your input abundances are normalised across replicates or not. RATs currently does not normalise across replicates, because proportions are be definition already normalised.\r\n2. A new overview plot maps the fold-change against the difference in proportion (`\"fcVSdprop\"`). Same caveat as above.\r\n3. Directly import from Salmon/Kallisto output using `fish4rodents()`. This saves a little time and a lot of memory, compared to importing via Sleuth.\r\n4. The volcano plot can now be done for genes, instead of for transcripts.\r\n5. In overview plots, DTU-positive points are always layered over the DTU-negative points, ensuring none are hidden.\r\n6. The histogram of effect sizes can be made for both transcripts and genes.\r\n7. A `scaling` factor for abundances is introduced. This could be useful when running RATs with TPM or similar normalised abundances, as 1 million transcripts is a gross under-estimation of the sample size (number of physical transcripts in the sequenced sample). If you can infer the sample size from your RNA preparation protocol, scaling the TPM accordingly would improve statistical power of RATS. Do not scale read-count abundances! Misuse of `scaling` will artificially inflate or deflate the significance of the observed differences, so use only if you know what you are doing and at your own risk!\r\n\r\n# Other improvements\r\n\r\n1. Styling tweaks to gene and overview plots to reduce clutter and improve encoding consistency.\r\n2. The summary reports are now presented as data.frames instead of named vectors. This makes them much more legible.\r\n3. The replicate lines in the gene plot are now slightly offset, to avoid becoming hidden by one another when the measurements are very similar.\r\n4. The interactive volcano plot now plots genes instead of transcripts. Hovering will provide brief info on the gene(s) under(/near) the pointer, clicking will pull up all the relevant information from the `$Genes` and `$Transcripts` tables for that gene and produce the relevant gene plot.\r\n5. The histogram of gene effect sizes now segregates positive and negative changes rather than showing the absolute values.\r\n6. General documentation improvements.\r\n7. Un-complicate parts of the code.\r\n8. Bootstrapping the replicates previously used a single sample from each condition \"as is\". This was not relatable to comparing one set of replicates against another and generally was extremely conservative and unhelpful. In this version, this alleviated by scaling the chosen samples by the number of samples per condition. \r\n\r\n# Bugfixes\r\n\r\n1. Restored table of contents for the vignettes.\r\n2. In the summaries, NA genes for transcript-level and both-levels tallies are now reported correctly instead of being always 0.\r\n3. Fixed some hard-coded field names that could cause failure with non-standard input field names.\r\n4. Better protection against entries in the annotation and abundances being in incompatible orders.\r\n\r\n# Other changes\r\n\r\n1. Optional dependency added for `wasabi`. Needed when importing data from Salmon.\r\n2. Plot improvements require `ggplot2` version >= 2.2.0.\r\n3. The use of multi-threading by-default by `data.table`, means that RATs now requires version >= 1.9.8 in order to prevent mismanagement of resources."}}
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