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add harmony integration #98

Merged
merged 4 commits into from
Jun 16, 2021
Merged

add harmony integration #98

merged 4 commits into from
Jun 16, 2021

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alexvpickering
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@alexvpickering alexvpickering commented Jun 14, 2021 •
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Background

Link to issue

BIOMAGE-699

Link to staging deployment URL

https://ui-alex-ui331-pipeline98.scp-staging.biomage.net/

Links to any Pull Requests related to this

hms-dbmi-cellenics/ui#331

Anything else the reviewers should know about the changes here

Changes

Code changes

Definition of DONE

Your changes will be ready for merging after each of the steps below have been completed:

Testing

  • Unit tests written
  • Tested locally with Inframock (with latest production data downloaded with biomage experiment pull)
  • Deployed to staging

To set up easy local testing with inframock, follow the instructions here: https://github.com/biomage-ltd/inframock
To deploy to the staging environment, follow the instructions here: https://github.com/biomage-ltd/biomage-utils

Documentation updates

Is all relevant documentation updated to reflect the proposed changes in this PR?

  • Relevant Github READMEs updated
  • Relevant wiki pages created/updated

Approvers

  • Approved by a member of the core engineering team
  • (UX changes) Approved by vickymorrison (this is her username, tag her if you need approval)

Just before merging:

Optional

  • Photo of a cute animal attached to this PR

@alexvpickering alexvpickering mentioned this pull request Jun 14, 2021
Merged
9 tasks
JuanluOnieva-biomage
JuanluOnieva-biomage reviewed Jun 15, 2021
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@JuanluOnieva-biomage JuanluOnieva-biomage left a comment

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It works perfectly Alex, great job. Only the comment about the PCs I leave to your choice. However, before approving, I remember that I made changes to the files (api/route-services/__mocks__/experiment.js and api/src/specs/models/processing-config-bodies/ProcessingConfigDataIntegration.v1.yaml) in the api when I added FastMNN. Even if the link works, could you update these files or peer with some engineer to see if we are continue using these files?

pipeline-runner/src/dataIntegration.r Outdated
scdata <- Seurat::RunPCA(scdata, npcs = 50, features = Seurat::VariableFeatures(object=scdata), verbose=FALSE)
if (!have.pca) {
scdata <- Seurat::ScaleData(scdata, verbose = FALSE)
scdata <- Seurat::RunPCA(scdata, verbose=FALSE)
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I would leave here the comment related to the default value of PCs, just to have it in mind.

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Thanks @JuanluOnieva-biomage I added the mocks for harmony in the api. I'm also going to refactor a bit as the integration function is getting a bit unwieldly.

@alexvpickering alexvpickering mentioned this pull request Jun 15, 2021
Merged
@alexvpickering alexvpickering merged commit 91839fa into develop Jun 16, 2021
@alexvpickering alexvpickering deleted the init-harmony branch June 16, 2021 16:43
ivababukova pushed a commit that referenced this pull request Jul 19, 2021
@kafkasl @alexvpickering
@JuanluOnieva-biomage @ogibson @dependabot @seb-mueller @xverges @aerlaut @cosa65 @robioson @StefanBabukov @marcellp
Release version 0.0.2 (#120)
4372389 
* add harmony integration (#98)

* add harmony

* refactor

* remove mistakes

* add dispersions for harmony

* Fix p.level (#102)

* Merge master into dev branch (#100)

* handle NA doublet scores (#61)

* Added no integration (#59)

* Added no integration

* Update qc-runner/src/dataIntegration.r

Co-authored-by: Juanlu <[email protected]>

Co-authored-by: Juanlu <[email protected]>

* Bump lodash from 4.17.20 to 4.17.21 in /local-runner (#58)

Bumps [lodash](https://github.com/lodash/lodash) from 4.17.20 to 4.17.21.
- [Release notes](https://github.com/lodash/lodash/releases)
- [Commits](lodash/lodash@4.17.20...4.17.21)

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump hosted-git-info from 2.8.8 to 2.8.9 in /local-runner (#64)

Bumps [hosted-git-info](https://github.com/npm/hosted-git-info) from 2.8.8 to 2.8.9.
- [Release notes](https://github.com/npm/hosted-git-info/releases)
- [Changelog](https://github.com/npm/hosted-git-info/blob/v2.8.9/CHANGELOG.md)
- [Commits](npm/hosted-git-info@v2.8.8...v2.8.9)

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Na doublet score (#62)

* handle NA doublet scores

* treat NA as doublet_score=0

* Add FastMNN step 6-7 (#60)

* Add FastMNN step 6-7

* Fix dockerfile

* Fix scdata

* change order

* Fix try-catch

* Change value to unisample and fastmnn

* Fix assay

* Add package

* Add dependencies

* Change to pak

* Add active.reduciton and pak

* Add var.explained

* Add comments

* Persist misc

* added improved error handling and traceback (#55)

* added improved error handling and traceback

* removed dump.frames

* no sample output for integration step

* moved state_fail_logic to withCallingHandlers block

* removed intended debug error

* Display the command used to launch docker from lambda (#63)

* Move GEM2S as a step in pipeline (#56)

* refactor wrapper

* Added gem2s functions to pipeline

* Adapted pipeline to new schema for gem2s

* renamed one task

* fixes for gem2s

* renamed qc-runner to pipeline-runner

* fixed tryCatch from rebase

* changed pipeline name to qc

* init upload-to-aws

* init meta_sets

* Added sample sets

* complete upload-to-aws

* add s3/dynamodb functions

* add buckets and tables

* writing input to meta.json file

* changed some pipeline references to gem2s/pipeline

* avoiding creating new containers for gem2s or qc if they already exist

* attaching both pipeline containers output (qc & gem2s) to pipeline process stdout

* just a lonenly runaway letter

* added dependencies

* typo

* make docker build for me

* send dynamodb items to api

* reflect nan bugfix from data-inegest

* temporarily fix for paws.common version 0.3.11

* change SNS messag type

* hotfix

* fix

* fix

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>

* Dependency issues and cellsets (#65)

Co-authored-by: Oliver Gibson <[email protected]>

* Add sns updates when tasks finish (#67)

Co-authored-by: Martin Fosco <[email protected]>

* fix per sample custom config (#66)

* fix per sample custom config

* loop through unique samples

* Fix seurat obj not found (#71)

* Sample ids property sent as list instead of string
* fix seurat_obj not found

Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Xavier Verges <[email protected]>

* Handle gem2s response refactoring (#68)

* Add sns updates when tasks finish

* Handle gem2s response refactoring

* Minor renaming

* Fix

* Fix

Co-authored-by: Martin Fosco <[email protected]>

* [BIOMAGE-1016] Sample uuids fix (#72)

* Sample ids property sent as list instead of string

* Fix

* Draft fix for uuids

* Fix

* fix

* fix

* checks

Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* Fix fast mnn (#75)

* Sample ids property sent as list instead of string

* Add FastMNN

* Restore 5_Upload-to-aws

* [BIOMAGE-1040] - Fix metadata structures (#74)

* fix data structures
* fix for empty metadata
Co-authored-by: Oliver Gibson <[email protected]>

* [BIOMAGE-1009] Fix error sns messages (#73)

* Refactor and add method dedicated to only sending sns error messages

* Add experimentId

* Move classifier to current position in ui

* Move into one single line

Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* Add experimentID and ingestionDate (#77)

* Add experimentID and ingestionDate

* Update comment

* Init filter stats (#76)

* init calc_filter_stats

* add filter stats for cellSizeDistribution

* return filter stats for all filter steps

* Test

* restore spacing for ease

* revert

* reverting spacing changes

* more de-change

* fix conflict

* check samples

Co-authored-by: Martin Fosco <[email protected]>

* move code from data-ingest (#78)

* fix mtcontent plotdata error (#79)

* new flow for releases (#83)

* added deployment for release/hotfixes PRs to master (#85)

* using tokens to allow flow to trigger testing

* Fix doublet settings (#81)

* test doublet settings

* Fix error in doublet scores config

Co-authored-by: Oliver Gibson <[email protected]>

* building releases/hotfixes on PR instead of push

* Fix determination of HOST_IP on Linux (#91)

* Fix determination of HOST_IP on Linux

* Replace spaces with tab

* Add tty flag to fix local output (#92)

* Update ci-develop.yaml

* Fix default doublet config (#82)

* use seed and fix config storage

* use scDblFinder to set default threshold

* remove gitignore

* remove debug

* change boolean logic

* Rm auto and enabled (#88)

* switch from orig.ident to samples (#95)

* Move to multipart upload (#94)

* Move to multipart upload

* Add print

* Fix progress-bar

* hardcode DEBUG_PATH (#93)

* hardcode DEBUG_PATH

* fix function name

* Remove hardcoded 10x (it is now hardcoded in the ui only) (#96)

Co-authored-by: Martin Fosco <[email protected]>

* re-enable per sample config (#97)

* added r.utils dependency install which is required by seurat-wrappers (#99)

* Deprecated change for ci.yaml

Co-authored-by: Alex Pickering <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>

* done i think (#101)

* Add build as a dependency of run (#103)

Also add new run-only target

* Init R package and test classifier filter (#104)

* init r package

* ignore debug

* remove file names within file

* use styler

* cleanup

* fix Dockerfile

* init filter_emptydrops tests

* fix introduced error for demo image

* add sample aware test

* update README; make task names look distinct

* update README

* update gem2s step messages

* add timer to gem2s steps

* Enable Slack build failure notifications

* Fix defaults (#109)

Co-authored-by: Oliver Gibson <[email protected]>

* Unlog y values (#112)

* unlog cellsizedistribution plot y values
* switch plot numbers to improve readibility

* Clean pipeline code (#105)

* Clean pipeline code

* Update pipeline-runner/R/gem2s-6-prepare_experiment.R

Co-authored-by: Alex Pickering <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* fixes

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Alex Pickering <[email protected]>

* Init filter high mito and filter gene umi outlier tests (#114)

* init filter_gene_umi_outlier tests

* init mito filter tests; fix calc_filter_stats

* Init cellszdoublet tests (#118)

* init filter_gene_umi_outlier tests

* init mito filter tests; fix calc_filter_stats

* Added tests for cellsize and doublets

* export filter_low_cellsize

* simplify parts of filter_low_cellsize

* restyle and update comment for filter_doublets test

* fix filter_doublets documentation

Co-authored-by: Alex Pickering <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* Removed embedding (#107)

* Removed embedding

* Update pipeline-runner/R/qc-7-embed_and_cluster.R

* Update pipeline-runner/R/qc-7-embed_and_cluster.R

* Update pipeline-runner/R/qc-7-embed_and_cluster.R

* Fix

Co-authored-by: Oliver Gibson <[email protected]>

* Fix (#113)

* Fix

* typo

Co-authored-by: Oliver Gibson <[email protected]>

* init renv (#110)

* try restore remoter docker-compose

* Update pipeline-runner/renv.lock.init

* Update pipeline-runner/renv.lock

* try update all packages

* Fix

* update README; remove R version

* harmony init lockfile

* fix

Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* Move defaultFilterSettings and missing per sample config additions to the pipeline (#119)

* Add defaultFilterSettings and per sample config for classifier and mito content

* Update gem2s-6-prepare_experiment.R

Co-authored-by: Martin Fosco <[email protected]>

Co-authored-by: Alex Pickering <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: StefanBabukov <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: Marcell Pek <[email protected]>
ivababukova pushed a commit that referenced this pull request Jul 20, 2021
@alexvpickering @JuanluOnieva-biomage
@kafkasl @ogibson @dependabot @seb-mueller @xverges @aerlaut @cosa65 @robioson @StefanBabukov @marcellp
Hotfix/fix master (#122)
c06d01f 
* add harmony integration (#98)

* add harmony

* refactor

* remove mistakes

* add dispersions for harmony

* Fix p.level (#102)

* Merge master into dev branch (#100)

* handle NA doublet scores (#61)

* Added no integration (#59)

* Added no integration

* Update qc-runner/src/dataIntegration.r

Co-authored-by: Juanlu <[email protected]>

Co-authored-by: Juanlu <[email protected]>

* Bump lodash from 4.17.20 to 4.17.21 in /local-runner (#58)

Bumps [lodash](https://github.com/lodash/lodash) from 4.17.20 to 4.17.21.
- [Release notes](https://github.com/lodash/lodash/releases)
- [Commits](lodash/lodash@4.17.20...4.17.21)

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Bump hosted-git-info from 2.8.8 to 2.8.9 in /local-runner (#64)

Bumps [hosted-git-info](https://github.com/npm/hosted-git-info) from 2.8.8 to 2.8.9.
- [Release notes](https://github.com/npm/hosted-git-info/releases)
- [Changelog](https://github.com/npm/hosted-git-info/blob/v2.8.9/CHANGELOG.md)
- [Commits](npm/hosted-git-info@v2.8.8...v2.8.9)

Signed-off-by: dependabot[bot] <[email protected]>

Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>

* Na doublet score (#62)

* handle NA doublet scores

* treat NA as doublet_score=0

* Add FastMNN step 6-7 (#60)

* Add FastMNN step 6-7

* Fix dockerfile

* Fix scdata

* change order

* Fix try-catch

* Change value to unisample and fastmnn

* Fix assay

* Add package

* Add dependencies

* Change to pak

* Add active.reduciton and pak

* Add var.explained

* Add comments

* Persist misc

* added improved error handling and traceback (#55)

* added improved error handling and traceback

* removed dump.frames

* no sample output for integration step

* moved state_fail_logic to withCallingHandlers block

* removed intended debug error

* Display the command used to launch docker from lambda (#63)

* Move GEM2S as a step in pipeline (#56)

* refactor wrapper

* Added gem2s functions to pipeline

* Adapted pipeline to new schema for gem2s

* renamed one task

* fixes for gem2s

* renamed qc-runner to pipeline-runner

* fixed tryCatch from rebase

* changed pipeline name to qc

* init upload-to-aws

* init meta_sets

* Added sample sets

* complete upload-to-aws

* add s3/dynamodb functions

* add buckets and tables

* writing input to meta.json file

* changed some pipeline references to gem2s/pipeline

* avoiding creating new containers for gem2s or qc if they already exist

* attaching both pipeline containers output (qc & gem2s) to pipeline process stdout

* just a lonenly runaway letter

* added dependencies

* typo

* make docker build for me

* send dynamodb items to api

* reflect nan bugfix from data-inegest

* temporarily fix for paws.common version 0.3.11

* change SNS messag type

* hotfix

* fix

* fix

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>

* Dependency issues and cellsets (#65)

Co-authored-by: Oliver Gibson <[email protected]>

* Add sns updates when tasks finish (#67)

Co-authored-by: Martin Fosco <[email protected]>

* fix per sample custom config (#66)

* fix per sample custom config

* loop through unique samples

* Fix seurat obj not found (#71)

* Sample ids property sent as list instead of string
* fix seurat_obj not found

Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Xavier Verges <[email protected]>

* Handle gem2s response refactoring (#68)

* Add sns updates when tasks finish

* Handle gem2s response refactoring

* Minor renaming

* Fix

* Fix

Co-authored-by: Martin Fosco <[email protected]>

* [BIOMAGE-1016] Sample uuids fix (#72)

* Sample ids property sent as list instead of string

* Fix

* Draft fix for uuids

* Fix

* fix

* fix

* checks

Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* Fix fast mnn (#75)

* Sample ids property sent as list instead of string

* Add FastMNN

* Restore 5_Upload-to-aws

* [BIOMAGE-1040] - Fix metadata structures (#74)

* fix data structures
* fix for empty metadata
Co-authored-by: Oliver Gibson <[email protected]>

* [BIOMAGE-1009] Fix error sns messages (#73)

* Refactor and add method dedicated to only sending sns error messages

* Add experimentId

* Move classifier to current position in ui

* Move into one single line

Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* Add experimentID and ingestionDate (#77)

* Add experimentID and ingestionDate

* Update comment

* Init filter stats (#76)

* init calc_filter_stats

* add filter stats for cellSizeDistribution

* return filter stats for all filter steps

* Test

* restore spacing for ease

* revert

* reverting spacing changes

* more de-change

* fix conflict

* check samples

Co-authored-by: Martin Fosco <[email protected]>

* move code from data-ingest (#78)

* fix mtcontent plotdata error (#79)

* new flow for releases (#83)

* added deployment for release/hotfixes PRs to master (#85)

* using tokens to allow flow to trigger testing

* Fix doublet settings (#81)

* test doublet settings

* Fix error in doublet scores config

Co-authored-by: Oliver Gibson <[email protected]>

* building releases/hotfixes on PR instead of push

* Fix determination of HOST_IP on Linux (#91)

* Fix determination of HOST_IP on Linux

* Replace spaces with tab

* Add tty flag to fix local output (#92)

* Update ci-develop.yaml

* Fix default doublet config (#82)

* use seed and fix config storage

* use scDblFinder to set default threshold

* remove gitignore

* remove debug

* change boolean logic

* Rm auto and enabled (#88)

* switch from orig.ident to samples (#95)

* Move to multipart upload (#94)

* Move to multipart upload

* Add print

* Fix progress-bar

* hardcode DEBUG_PATH (#93)

* hardcode DEBUG_PATH

* fix function name

* Remove hardcoded 10x (it is now hardcoded in the ui only) (#96)

Co-authored-by: Martin Fosco <[email protected]>

* re-enable per sample config (#97)

* added r.utils dependency install which is required by seurat-wrappers (#99)

* Deprecated change for ci.yaml

Co-authored-by: Alex Pickering <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Juanlu <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>

* done i think (#101)

* Add build as a dependency of run (#103)

Also add new run-only target

* Init R package and test classifier filter (#104)

* init r package

* ignore debug

* remove file names within file

* use styler

* cleanup

* fix Dockerfile

* init filter_emptydrops tests

* fix introduced error for demo image

* add sample aware test

* update README; make task names look distinct

* update README

* update gem2s step messages

* add timer to gem2s steps

* Enable Slack build failure notifications

* Fix defaults (#109)

Co-authored-by: Oliver Gibson <[email protected]>

* Unlog y values (#112)

* unlog cellsizedistribution plot y values
* switch plot numbers to improve readibility

* Clean pipeline code (#105)

* Clean pipeline code

* Update pipeline-runner/R/gem2s-6-prepare_experiment.R

Co-authored-by: Alex Pickering <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* Update pipeline-runner/R/gem2s-helpers.R

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

* fixes

* Update pipeline-runner/R/gem2s-helpers.R

Co-authored-by: Alex Pickering <[email protected]>

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Alex Pickering <[email protected]>

* Init filter high mito and filter gene umi outlier tests (#114)

* init filter_gene_umi_outlier tests

* init mito filter tests; fix calc_filter_stats

* Init cellszdoublet tests (#118)

* init filter_gene_umi_outlier tests

* init mito filter tests; fix calc_filter_stats

* Added tests for cellsize and doublets

* export filter_low_cellsize

* simplify parts of filter_low_cellsize

* restyle and update comment for filter_doublets test

* fix filter_doublets documentation

Co-authored-by: Alex Pickering <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* Removed embedding (#107)

* Removed embedding

* Update pipeline-runner/R/qc-7-embed_and_cluster.R

* Update pipeline-runner/R/qc-7-embed_and_cluster.R

* Update pipeline-runner/R/qc-7-embed_and_cluster.R

* Fix

Co-authored-by: Oliver Gibson <[email protected]>

* Fix (#113)

* Fix

* typo

Co-authored-by: Oliver Gibson <[email protected]>

* init renv (#110)

* try restore remoter docker-compose

* Update pipeline-runner/renv.lock.init

* Update pipeline-runner/renv.lock

* try update all packages

* Fix

* update README; remove R version

* harmony init lockfile

* fix

Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>

* Move defaultFilterSettings and missing per sample config additions to the pipeline (#119)

* Add defaultFilterSettings and per sample config for classifier and mito content

* Update gem2s-6-prepare_experiment.R

Co-authored-by: Martin Fosco <[email protected]>

* init density kneeplot data (#111)

* init density kneeplot data

* update plot

* use unique fdr/ranks

* get_bcranks_plot_data works

* fix

* Fix

* Rollback unnecessary empty plot data addition

Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>

* fix empty guidata case

Co-authored-by: Juanlu <[email protected]>
Co-authored-by: Pol Alvarez <[email protected]>
Co-authored-by: ogibson-biomage <[email protected]>
Co-authored-by: dependabot[bot] <49699333+dependabot[bot]@users.noreply.github.com>
Co-authored-by: seb-mueller <[email protected]>
Co-authored-by: Xavier Vergés <[email protected]>
Co-authored-by: Oliver Gibson <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: Anugerah Erlaut <[email protected]>
Co-authored-by: Martin Fosco <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: StefanBabukov <[email protected]>
Co-authored-by: James Robinson <[email protected]>
Co-authored-by: Marcell Pek <[email protected]>
alexvpickering pushed a commit that referenced this pull request Jan 4, 2023
@saracastel
Merge pull request #98 from biomage-org/2254-subset-metadata
02a7c26 
[BIOMAGE 2254] - Refactor cellset creation for subset experiment
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@JuanluOnieva-biomage JuanluOnieva-biomage JuanluOnieva-biomage approved these changes

@ogibson ogibson Awaiting requested review from ogibson

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@alexvpickering @JuanluOnieva-biomage