biopipen

• 🐛 [scrna.SeuratClusterStats] Fix toc not saved correct (causing report not including the right sections)

What's Changed

• 🔖 0.20.4 by @pwwang in https://github.com/pwwang/biopipen/pull/89

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.3...0.20.4

• 🐛 [scrna.SeuratPreparing] Fix when cell_qc is None
• 🎨 [scrna.MarkersFinder] Add margins to volcano plot
• 🐛 [scrna.SeuratClusterStats] Fix ident in cases of envs.dimplots not working

What's Changed

• 🔖 0.20.3 by @pwwang in https://github.com/pwwang/biopipen/pull/88

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.2...0.20.3

• 🚑 [scrna.SeuratPreparing] Fix % in docstring to crash the pipeline

What's Changed

• 🔖 0.20.2 by @pwwang in https://github.com/pwwang/biopipen/pull/87

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.1...0.20.2

• 📝 [scrna_basic/scrna_metabolic_landscape/scrna/tcr] Update docstring
• 🎨 [scrna.MarkersFinder] Try include more genes in volcano plot (pwwang/immunopipe#17)
• 🎨 [scrna.CellsDistribution] Give better error message in CellsDistribution if group value not found (pwwang/immunopipe#16)
• 🚚 [tcr.TCRClusterStats] Rename TCRClusteringStats to TCRClusterStats (pwwang/immunopipe#15)

What's Changed

• 🔖 0.20.1 by @pwwang in https://github.com/pwwang/biopipen/pull/86

Full Changelog: https://github.com/pwwang/biopipen/compare/0.20.0...0.20.1

⬆️ Bump pipen to 0.12

What's Changed

• 🔖 0.20.0 by @pwwang in https://github.com/pwwang/biopipen/pull/85

Full Changelog: https://github.com/pwwang/biopipen/compare/0.19.0...0.20.0

• ⬆️ Bump pipen-report 0.13.1 (pwwang/immunopipe#9, 2)
• 💄 [docs] Hide unnecessary items in nav bar
• 💄 [docs] Get docs, especially API docs, formatted better
• 🎨 [scrna.SeuratPreparing] Improve QC plots
• 📝 [scrna.SeuratPreparing] Fix type annotation for envs.features_defaults.ncol in docstring
• 🐛 [scrna.CellsDistribution] Fix the cluster order in pie charts
• 🐛 [scrna.SeuratClusterStats] Fix the cluster order in pie charts
• 🐛 [delim.SampleInfo] Fix order in pie charts
• ✨ [scrna.SeuratClustering] Add number of clusters at the end of log
• 📝 [tcr.Immunarch] Fix docstring for envs.div.args
• ✨ [scrna.SeuratClusterStats] Allow mutiple columns in the file for envs.features_defaults.features
• ⬆️ Bump pipen-board to 0.12.5
• 🎨 [delim.SampleInfo] Add stricter checker for input file (pwwang/immunopipe#13)
• 🎨 [tcr.CloneResidency] Allow order to be optional
• 🎨 [scrna.SeuratClusterStats] Indicate the case name in logs when pie is enable for group-by
• 🎨 [tcr.Immunarch] Allow to skip overlap and gene usage analyses by setting method to none (pwwang/immunopipe#11, pwwang/immunopipe#12)
• 🐛 [tcr.TCRClusteringStats] Don't cluster on heatmap when there are only 2 samples
• 🐛 [scrna_metabolic_landscape.MetabolicFeatures] Import Seurat explictly to avoid satijalab/seurat#2853
• 🐛 [scrna_metabolic_landscape.MetabolicPathwayActivity] Fix when NA values in data for heatmap
• 🐛 [scrna_metabolic_landscape.MetabolicPathwayHeterogeneity] Fix error when no significant pathways selected
• 🩹 [scrna.ModuleScoreCalculator] Set default assay to RNA in case module scores only caculated using integrated features

What's Changed

• 🔖 0.19.0 by @pwwang in https://github.com/pwwang/biopipen/pull/84

Full Changelog: https://github.com/pwwang/biopipen/compare/0.18.3...0.19.0

• 🐛 [scrna.MarkersFinder] Fix when either ident is empty

What's Changed

• 🔖 0.18.3 by @pwwang in https://github.com/pwwang/biopipen/pull/83

Full Changelog: https://github.com/pwwang/biopipen/compare/0.18.2...0.18.3

• 🐛 [tcr.CDR3AAphyschem.R] Fix a bug when the min length of CDR3 seqs > 12

What's Changed

• 🔖 0.18.2 by @pwwang in https://github.com/pwwang/biopipen/pull/82

Full Changelog: https://github.com/pwwang/biopipen/compare/0.18.1...0.18.2

• ⬆️ Bump datar to 0.15.3
• 🎨 [scrna.MetaMarkers/ScFGSEA/SeuratClusterStats] Remove tidyseurat:: prefix for filter
• ✨ [tcr.TESSA] Allow the results to be saved to seurat object
• 📝 [tcr.TESSA] Fix docs about envs.assay

What's Changed

• 🔖 0.18.1 by @pwwang in https://github.com/pwwang/biopipen/pull/81

Full Changelog: https://github.com/pwwang/biopipen/compare/0.18.0...0.18.1

• 🔧 Update .gitignore
• ⬆️ Bump pipen to 0.11
• ⬆️ Bump datar to 0.15.2
• 🚨 Make line length to 88 for linting
• ✨ [core.filters] Add skip argument to r()
• 🚑 [tcr.TESSA] Fix type annotation for envs.max_iter
• 🐛 [delim.SampleInfo] Allow unique: prefix for on in stats cases; fix sample order in plots
• ♻️ [scrna.SeuratClusterStats] Redesign envs
• ✨ [scrna.MarkersFinder] Add volcano plot
• ✨ [tcr.TESSA] Add envs.assay for seurat object input
• 🐛 [tcr.TESSA] Fix when a V-gene/J-gene is missing
• ✅ [gsea.FGSEA] Fix tests
• 🚸 [scrna.SeuratClustering] Add clear message when k.weight is too large for IntegrateData

What's Changed

• 🔖 0.18.0 by @pwwang in https://github.com/pwwang/biopipen/pull/80

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.7...0.18.0

• ⬆️ Bump pipen-board to 0.11.7
• ✅ [tests] Allow pass FORCE=true to run local-only tests
• ✅ [tests] Fix receiving VERBOSE and FORCE in test script
• 🚑 [tcr.ImmunarchLoading] Fix when Sample is the only column in meta
• ✨ [tcr.TESSA] Add process and test

What's Changed

• 🔖 0.17.7 by @pwwang in https://github.com/pwwang/biopipen/pull/79

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.6...0.17.7

• 👷 Fix CI for publishing the package
• ⬆️ Bump pipen-board to 0.11.5
• 🚑 [scrna.SeuratClusterStats] Adjust default width and height for plots
• 🚑 [scrna.CellTypeAnnotation] Keep order of clusters after hitype annotation

What's Changed

• 🔖 0.17.6 by @pwwang in https://github.com/pwwang/biopipen/pull/78

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.5...0.17.6

• 👷 Do not run CI build for publish job
• 🎨 [tcr.TCRClustering] Add TCR_Cluster_Size1 in addition to TCR_Cluster_Size in out.clusterfile to represent #cells and #CDR3 seqs
• ⬆️ Bump up dependencies

What's Changed

• 🔖 0.17.5 by @pwwang in https://github.com/pwwang/biopipen/pull/77

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.4...0.17.5

• ✨ [tcr.TCRClustering] Add TCR_Cluster_Size in out.clusterfile
• 💥 [scrna.SeuratClusterStats] Rename envs.exprs to envs.features

What's Changed

• 🔖 0.17.4 by @pwwang in https://github.com/pwwang/biopipen/pull/76

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.3...0.17.4

• ⬆️ Bump pipen-report to 0.12.8
• 📝 [delim.SampleInfo] Show h1 in report only when stats specified
• 📝 [delim.SampleInfo] Fix parsing excluded_cols in report

What's Changed

• 🔖 0.17.3 by @pwwang in https://github.com/pwwang/biopipen/pull/75

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.2...0.17.3

• 📝 [delim.SampleInfo] Add report template

What's Changed

• 🔖 0.17.2 by @pwwang in https://github.com/pwwang/biopipen/pull/74

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.1...0.17.2

• 🎨 [scrna.CellTypeAnnotation] Change seurat_clusters_old to seurat_clusters_id to save old seurat_clusters
• 💥 [csv] Rename to delim
• 🚚 [csv.BindRows] Rename to delim.RowsBinder
• ✨ [utils.mutate_helpers.R] Add paired() to identify paired records
• ✨ [delim.SampleInfo] Add process

What's Changed

• 🔖 0.17.1 by @pwwang in https://github.com/pwwang/biopipen/pull/73

Full Changelog: https://github.com/pwwang/biopipen/compare/0.17.0...0.17.1

• ⬆️ Bump pipen-board to 0.11.4
• 📝 [docs] Update logo
• 📝 [docs] Add css due to mkdocs-rtd change
• 💥 [core.filters] Default sortkeys to False for filter r
• 🐛 [scrna.ModuleScoreCalculator] Fix aggregation values of programs
• 🐛 [scrna.SeuratClusterStats] Fix typo for default stats
• 🐛 [scrna.ModuleScoreCalculator] Fix name for cell cycle scores
• 🐛 [scrna.CellsDistribution] Fix when cells_by or group_by is not an identifier
• 🚑 [utils.mutate_helpers.R] Allow accessing metadata using .
• ✨ [scrna.ModuleScoreCalculator] Add proc

What's Changed

• 🔖 0.17.0 by @pwwang in https://github.com/pwwang/biopipen/pull/72

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.7...0.17.0

• 🔥 [scrna.SeuratMetadataMutater] Remove unnecessary in.mutaters
• 📝 [docs] Use kmdocs-rtd for documentation
• 📝 [scrna_basic] Fix docs
• 📝 [docs] Fix CI when files in docs/ changes
• 📝 [docs] Fix CI when CI config file changes
• 📝 [scrna_basic] Update docs for processes
• 🔧 [scrna_basic] Update example config file
• 📝 [docs] Add logo and favicon
• 📝 [docs] Fix font-sizes in APIs
• 📝 [docs] Fix logo size in README

What's Changed

• 0.16.7 by @pwwang in https://github.com/pwwang/biopipen/pull/71

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.6...0.16.7

• 🚑 [scrna] Hotfix for docstring when parsed by argparse help

What's Changed

• 0.16.6 by @pwwang in https://github.com/pwwang/biopipen/pull/70

Full Changelog: https://github.com/pwwang/biopipen/compare/0.16.5...0.16.6