fix(vignette): fix incorrect CRAN links in the Introduction vignette refactor(data): make the data smaller in order to follow the CRAN guidelines refactor(web): fix paths to the moved Basic Analysis vignette refactor(vignette): remove the Basic Analysis vignette from the CRAN pacakge refactor(vignette): add the tracking visualisation to the single-cell vignette fix(vignette): remove https because it fails on CRAN checks feat(upkeep): update README & NAMESPACE to reflect the single-cell support and also shorten the documentation for readability fix(io): fix imports fix(single-cell): fix the missing barcode column feat(data): add the "scdata" dataset with paired chain data and barcodes docs(io): update docs for repLoad / repSave to reflect single-cell support docs(single-cell): add docs for select_barcodes feat(vignette): finish the single-cell vignette feat(vignette): add a draft for the single-cell vignette refactor(upkeep): add "single-cell" and "data" commit scopes feat(io): add a paired chain parsing support for 10X feat(data): add new test files for single-cell docs(single-cell): add docs for single-cell functions docs(upkeep): update the docs for bulk data feat(upkeep): add the single-cell example data feat(web): add the single-cell vignette feat(single-cell): add a support for filtering and selecting clonotypes by barcodes and the Seurat::Idents() output refactor(io): remove raw_contig and raw_clonotype columns from 10X data to reduce the memory print feat(upkeep): add a new environment for additional immunarch columns fix(io): update the repLoad docs feat(io): add the ".coding" argument to filter out non-coding sequences (ON by default) chore(vignette): add badges for the optimisation of looking for downloads statistics chore(tools): move filter_barcodes() to singlecell.R and rename it to select_barcodes() chore(db): rename search.R with annotation.R chore(pub-rep): rename shared.R to public.R chore(tools): rename processing.R to sampling.R chore(data): move the description of "immdata" to data_docs.R chore(tools): move data filtering & manipulation functions to the preprocessing.R file refactor(io) / refactor(vignette): focus on the automatic detection of file formats refactor(upkeep): change authors to contributors feat(io): add "report" and "vdjca" files to the ignore list refactor(io): put a warning when .format is provided, and update repLoad documentation skip this comment in NEWS: add IO_REFACTOR label to where I experimented with data.table-based input reading. Initial benchmarks shows x2 acceleration in data loading speed fix(vis): fix a bug #65 in plotting repClonality with .col="nt" (PR #66 from Rushil) refactor(upkeep): add pull requests names to the contribution guide fix(vis): fix a bug in clonality visualisations #65 (PR #66) refactor(upkeep): update the contribution guide refactor(vignette): remove treemap and replace gridExtra with patchwork refactor(vis): remove treemap and replace gridExtra with patchwork fix(vignette): replace "develop" with "dev" refactor(tools): add_class() now adds the class to the beginning of the class attributes in order to comply with the R class system feat(vignette): cosmetic changes to the README feat(upkeep): add the pkgdown folder to the ignore feat(upkeep): remove "Home" and "News", add a link to the covid-19 repo feat(vignette): make the README more succinct, add a quick start section and the visitors badge refactor(upkeep): minor changes in text feat(upkeep): add the tag for the website refactor(io): refactor warning messages to make them more correct & add "na.rm = TRUE" to eliminates NAs when computing new Proportion columns
", "publication_date": "2020-06-15", "publisher": "Zenodo", "related_identifiers": [ { "identifier": "https://github.com/immunomind/immunarch/tree/0.6.5", "relation_type": { "id": "issupplementto", "title": { "de": "Erg\u00e4nzt", "en": "Is supplement to" } }, "scheme": "url" } ], "resource_type": { "id": "software", "title": { "de": "Software", "en": "Software" } }, "rights": [ { "description": { "en": "" }, "id": "other-open", "title": { "en": "Other (Open)" } } ], "title": "immunomind/immunarch: 0.6.5: Basic single-cell support", "version": "0.6.5" }, "parent": { "access": { "owned_by": { "user": "12487" }, "settings": { "accept_conditions_text": null, "allow_guest_requests": false, "allow_user_requests": false, "secret_link_expiration": 0 } }, "communities": { "default": "10f33f78-3f29-41b6-bb10-f757a8f03cb8", "entries": [ { "access": { "member_policy": "open", "members_visibility": "public", "record_submission_policy": "open", "review_policy": "open", "visibility": "public" }, "children": { "allow": false }, "created": "2020-03-16T11:40:44.487619+00:00", "custom_fields": {}, "deletion_status": { "is_deleted": false, "status": "P" }, "id": "10f33f78-3f29-41b6-bb10-f757a8f03cb8", "links": {}, "metadata": { "curation_policy": "The Coronavirus Disease Research Community - COVID-19 is curated by a selected team of experts nominated by OpenAIRE* (see list below). Each time a Zenodo user wants to add a record into the community, an email is sent to the curators that will decide whether to include the record or not.
\r\n\r\nOnly records that may be relevant to the Corona Virus Disease (COVID-19) or the SARS-CoV-2 should be included in this community. The Community curators are not able to edit records, therefore they may ask the corresponding authors to modify the record metadata when necessary, to provide the readers/users with more detailed information according to the FAIR principle of Open Science.
\r\n\r\nIf after its acceptance, a record is subsequently found not to be compliant, we reserve the right to remove it from the community.
\r\n\r\nThe curation team is reachable through the following email address for further clarification or information: covid19@openaire.eu.
\r\n\r\nCurator List:
\r\n\r\n* OpenAIRE: open access and open science training and support since 2009. OpenAIRE is the largest aggregator of European Commission funded research outputs and beyond, also delivering on-demand services for research communities.
\r\n", "page": "This community collects research outputs that may be relevant to the Coronavirus Disease (COVID-19) or the SARS-CoV-2. Scientists are encouraged to upload their outcome in this collection to facilitate sharing and discovery of information. Although Open Access articles and datasets are recommended, also closed and restricted access material are accepted. All types of research outputs can be included in this Community (Publication, Poster, Presentation, Dataset, Image, Video/Audio, Software, Lesson, Other).
\r\n\r\nThe recent Corona Virus Disease (COVID-19) outbreak is requiring unseen efforts of collaboration of the scientific community that need to act fast and to share results in an unpredictable manner. In order to facilitate the Scientist efforts, this community was created to collect all research results that could be relevant for the scientific community working on the Corona Virus Disease (COVID-19) and SARS-CoV-2.
\r\n\r\nAlthough Open Access articles and datasets are recommended, also closed and restricted access material are accepted. All types of research outputs can be included in this Community (Publication, Poster, Presentation, Dataset, Image, Video/Audio, Software, Lesson, Other).
\r\n\r\nWhen depositing a resource that is linked to other resources (not limited to the records deposited in Zenodo but also in other repositories), please make sure that your record is linked to all the other related elements already available, in order to adhere to the FAIR principles of Open Science to maximise the reusability of research results.
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