{"action":"created","issue":{"url":"https://api.github.com/repos/hbc/bcbioSingleCell/issues/64","repository_url":"https://api.github.com/repos/hbc/bcbioSingleCell","labels_url":"https://api.github.com/repos/hbc/bcbioSingleCell/issues/64/labels{/name}","comments_url":"https://api.github.com/repos/hbc/bcbioSingleCell/issues/64/comments","events_url":"https://api.github.com/repos/hbc/bcbioSingleCell/issues/64/events","html_url":"https://github.com/hbc/bcbioSingleCell/pull/64","id":329507440,"node_id":"MDExOlB1bGxSZXF1ZXN0MTkyNzQ2NTMw","number":64,"title":"v0.1.14","user":{"login":"mjsteinbaugh","id":1760218,"node_id":"MDQ6VXNlcjE3NjAyMTg=","avatar_url":"https://avatars1.githubusercontent.com/u/1760218?v=4","gravatar_id":"","url":"https://api.github.com/users/mjsteinbaugh","html_url":"https://github.com/mjsteinbaugh","followers_url":"https://api.github.com/users/mjsteinbaugh/followers","following_url":"https://api.github.com/users/mjsteinbaugh/following{/other_user}","gists_url":"https://api.github.com/users/mjsteinbaugh/gists{/gist_id}","starred_url":"https://api.github.com/users/mjsteinbaugh/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/mjsteinbaugh/subscriptions","organizations_url":"https://api.github.com/users/mjsteinbaugh/orgs","repos_url":"https://api.github.com/users/mjsteinbaugh/repos","events_url":"https://api.github.com/users/mjsteinbaugh/events{/privacy}","received_events_url":"https://api.github.com/users/mjsteinbaugh/received_events","type":"User","site_admin":false},"labels":[],"state":"open","locked":false,"assignee":null,"assignees":[],"milestone":null,"comments":1,"created_at":"2018-06-05T15:23:29Z","updated_at":"2018-06-05T15:46:47Z","closed_at":null,"author_association":"MEMBER","pull_request":{"url":"https://api.github.com/repos/hbc/bcbioSingleCell/pulls/64","html_url":"https://github.com/hbc/bcbioSingleCell/pull/64","diff_url":"https://github.com/hbc/bcbioSingleCell/pull/64.diff","patch_url":"https://github.com/hbc/bcbioSingleCell/pull/64.patch"},"body":"## Major changes\r\n\r\n- Multiplexed [Cell Ranger][] barcodes are now reformatted to be more readable\r\n  and compatible with the `mapCellsToSamples()` utility function. This change\r\n  helps simplify the internal code for `cell2sample()`. For example in the\r\n  pbmc4k dataset, the barcode IDs are sanitized from `TTTGGTTTCGCTAGCG-1` to\r\n  \"`pbmc4k_1_TTTGGTTTCGCTAGCG`\". The \"`1`\" here denotes 1 sample in the matrix,\r\n  which is how [Cell Ranger][] denotes multiplexed samples in a single counts\r\n  matrix. Note that the \"`-`\" character is illegal in names, so we consistently\r\n  sanitize barcodes to contain \"`_`\" instead. See `help(\"make.names\")` for\r\n  more information on syntactically valid names in [R][].\r\n- `readCellRanger()` no longer requires reference data defined by `refdataDir`,\r\n  although this is still recommended.\r\n\r\n## Minor changes\r\n\r\n- Resaved example datasets.\r\n- Switched the example `cellranger_small` and `seurat_small` datasets to the\r\n  publicly available pbmc4k dataset from 10X Genomics. Here we've subset the\r\n  top 500 cells and genes by abundance. We'll use either the pbmc4k or pbmc8k\r\n  dataset for the vignette in a future update.\r\n- `bcbioSingleCell()` and `readCellRanger()` functions now consistently default\r\n  to not requiring `sampleMetadataFile`, which is now `NULL` by default. For\r\n  `bcbioSingleCell()`, if a custom sample metadata file is not provided, the\r\n  function reads from the bcbio YAML metadata. For `readCellRanger()`, the\r\n  function uses `minimalSampleData()` internally to return minimal metadata,\r\n  containing `sampleName` and `description` columns.\r\n- Broke out internal `.sampleDirs()` function to `bcbioSingleCell()` and\r\n  `readCellRanger()` functions.\r\n- Improved `plotMarker` documentation examples to use mitochondrial genes.\r\n- Using `seurat_small` in place of `Seurat::pbmc_small` in working examples.\r\n  \r\n## Internal code changes\r\n\r\n- Now consistently using [dplyr][] for piped `data.frame` as much as possible,\r\n  where applicable. Code is being updated to use [tidyeval][]."},"comment":{"url":"https://api.github.com/repos/hbc/bcbioSingleCell/issues/comments/394760327","html_url":"https://github.com/hbc/bcbioSingleCell/pull/64#issuecomment-394760327","issue_url":"https://api.github.com/repos/hbc/bcbioSingleCell/issues/64","id":394760327,"node_id":"MDEyOklzc3VlQ29tbWVudDM5NDc2MDMyNw==","user":{"login":"lintr-bot","id":10925265,"node_id":"MDQ6VXNlcjEwOTI1MjY1","avatar_url":"https://avatars3.githubusercontent.com/u/10925265?v=4","gravatar_id":"","url":"https://api.github.com/users/lintr-bot","html_url":"https://github.com/lintr-bot","followers_url":"https://api.github.com/users/lintr-bot/followers","following_url":"https://api.github.com/users/lintr-bot/following{/other_user}","gists_url":"https://api.github.com/users/lintr-bot/gists{/gist_id}","starred_url":"https://api.github.com/users/lintr-bot/starred{/owner}{/repo}","subscriptions_url":"https://api.github.com/users/lintr-bot/subscriptions","organizations_url":"https://api.github.com/users/lintr-bot/orgs","repos_url":"https://api.github.com/users/lintr-bot/repos","events_url":"https://api.github.com/users/lintr-bot/events{/privacy}","received_events_url":"https://api.github.com/users/lintr-bot/received_events","type":"User","site_admin":false},"created_at":"2018-06-05T15:46:47Z","updated_at":"2018-06-05T15:46:47Z","author_association":"NONE","body":"[R/readCellRanger.R:194:1:](https://github.com/hbc/bcbioSingleCell/blob/4df4b6afc15a36c61a1f5b4e1166af0ffb10afec/R/readCellRanger.R#L194) *style:* **Lines should not be more than 80 characters.**\n```r\n​        # in the refdata directory. It will also drop genes that are now dead in the\n^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test_differential_expression_functions.R:53:11:](https://github.com/hbc/bcbioSingleCell/blob/4df4b6afc15a36c61a1f5b4e1166af0ffb10afec/tests/testthat/test_differential_expression_functions.R#L53) *style:* **Commented code should be removed.**\n```r\n​#         caller = \"DESeq2\"\n          ^~~~~~~~~~~~~~~~~\n```\n[tests/testthat/test_differential_expression_functions.R:55:7:](https://github.com/hbc/bcbioSingleCell/blob/4df4b6afc15a36c61a1f5b4e1166af0ffb10afec/tests/testthat/test_differential_expression_functions.R#L55) *style:* **Commented code should be removed.**\n```r\n​#     expect_s4_class(x, \"DESeqResults\")\n      ^~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~\n```"}}
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