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CHANGELOG

v1.3.1 (2024-01-31)

Build

  • build: Update artifact destination for production (e05d487)

Fix

  • fix: Update version in DESCRIPTION, update package name in meta.yaml, and rm tar.gz in package (092ecfb)

Unknown

  • Merge pull request #143 from NIDAP-Community/dev

Removed tarballs, updated version number and Conda package name (6787e97)

  • Merge pull request #142 from NIDAP-Community/update_cd

build: Update artifact destination for production (f0e24ad)

  • Merge pull request #140 from NIDAP-Community/update_cd

fix: Update version in DESCRIPTION, update package name in meta.yaml,… (485131c)

v1.3.0 (2024-01-30)

Documentation

  • docs(version): Automatic development release (0f85910)

Feature

  • feat: CI/CD and Conda Recipe (ae18de3)

  • feat: Updates to QC flag print out and associated markdown vignettes, tests, and fixtures (f3f5879)

  • feat: QC output for specific flagged segments and probes (6f434ab)

  • feat(segmentID list): Added initial list of segment IDs before filtering (3f6c011)

  • feat(DEG): Added linear model (no random effect) in DEG analysis and adjusted output table (e995733)

Fix

  • fix(docs): Updated function documentation (d69b216)

  • fix(filtering): Updates for sankey plot in filtering (995b40d)

  • fix(study design): Updated Sankey plot for updated ggplot2 and ggforce versions (7270e32)

  • fix(DESCRIPTION): Setting explicit versions for depends ggplot2, ggforce to fix plotting issue (e09371f)

  • fix(DESCRIPTION): Relaxed version spec for depends (2c8b69a)

  • fix(DESCRIPTION): Updated dependencies in DESCRIPTION to be imports not depends (eedb3e3)

  • fix: install bioconductor packages

see https://bioinformatics.stackexchange.com/a/3375 (f484033)

  • fix(kidney integration test): Updated kidney test markdown for testing new filtering features (9fd601f)

  • fix(DEG): format change (6e4482a)

  • fix(DEG): New config for yml file (65f7614)

  • fix(DEG): changed error checking code (eeeecd1)

Unknown

  • Merge pull request #139 from NIDAP-Community/dev

Testing Continuous Deployment to NIDAP (5d5d914)

  • Merge pull request #138 from NIDAP-Community/update_cd

feat: CI/CD and Conda Recipe (a675d0b)

  • Merge pull request #137 from NIDAP-Community/QC_flag_report_feature

Qc flag report feature (046f5e6)

Conflicts: vignettes/Integration_Test_Kidney.Rmd (3fab7b1)

  • Kidney Integration test: Update for QC parameters (b880f9e)

  • Merge pull request #136 from NIDAP-Community/defix_830

Defix 830 (25cd950)

  • Merge branch 'dev' into defix_830

Signed-off-by: Ned Cauley <[email protected]> (5bebe06)

  • Merge pull request #135 from NIDAP-Community/filter_segment_selection

Filter segment selection (62140eb)

  • Merge branch 'dev' into filter_segment_selection

Signed-off-by: Ned Cauley <[email protected]> (df9ac61)

  • Merge pull request #134 from NIDAP-Community/fix_sankey

Fix sankey (b96dba8)

  • Merge pull request #133 from NIDAP-Community/fix_dependencies

Fix dependencies (b1719d0)

Dev (f9deb63)

  • Merge pull request #125 from NIDAP-Community/bioc

fix: install bioconductor packages (d013780)

  • Merge pull request #130 from NIDAP-Community/dev

Dev (9ea4353)

  • Merge pull request #129 from NIDAP-Community/fix_dependencies

fix(DESCRIPTION) (4adf523)

  • fix(initialization):Added slide name to segmentID (2322b1e)

  • Merge pull request #123 from NIDAP-Community/linear_model_de

feat(initialization):Added segmentID creation (8a3453a)

  • feat(initialization):Added segmentID creation (b613d7d)

  • Merge pull request #122 from NIDAP-Community/dev

Dev (0830ab9)

  • Merge pull request #121 from NIDAP-Community/linear_model_de

fix(doc):Updated version number (c65bc5b)

  • fix(doc):Updated version number (4ad6f29)

  • Merge pull request #120 from NIDAP-Community/dev

Dev (c2337f9)

  • Merge pull request #119 from NIDAP-Community/linear_model_de

Added linear model (no random effect) in DEG analysis (ed70388)

  • Merge pull request #117 from NIDAP-Community/dev

Update description to 1.1.1 (2691689)

  • Merge pull request #116 from NIDAP-Community/update_description

fix (DESCRIPTION): Updated description to version 1.1.1 (7c38039)

  • fix (DESCRIPTION): Updated description to version 1.1.1 (33f341d)

  • Merge pull request #115 from NIDAP-Community/dev

Dev (a8cebab)

  • Merge pull request #114 from NIDAP-Community/sankey_update

Updated filtering with new Sankey parameter (b5675af)

  • feat (filtering): Added parameter and adjusted function to exlude slide from Sankey (f082802)

  • Merge pull request #113 from NIDAP-Community/sankey_update

Added parameter for excluding slide from sankey (20fb59f)

  • feat (study design): Added parameter and adjusted function for optionally excluding slide from Sankey plot (7a4906b)

  • Merge branch 'CPTR_dataset' into dev

Signed-off-by: Ned Cauley <[email protected]> (17670b3)

  • Merge pull request #110 from NIDAP-Community/filtering

Fixes for filtering: genes of interest table print, parameters for segment gene detection and study gene detection, Sankey plot update (424456d)

  • fix (test-filtering): Updated test and helper for new Filtering parameters (c54fff1)

  • fix (filtering): Sankey plot adjusted to match Study Design (4cb09be)

  • Added missing parameters for cutoffs for gene detetion per segment and per whole study, restructured script for these new parameters (a072c4c)

  • fix (filtering): Added defaults for parameters, cleaned up error messages and variable names, and fixed print for goi table (e91506a)

  • Merge branch 'main' into CPTR_dataset (1593667)

  • test (Kidney integration): Changed fixture creation back to FALSE, should not default to fixture creation (ad16183)

  • test (CPTR Integration): Added goi list for DEG analysis and fixed variable names so that all units run (4005391)

  • Added GOI table printing for Filtering (2a7be1a)

  • Started CPTR vignette and added fixtures (0abf579)

  • Merge pull request #109 from NIDAP-Community/dev

Dev (3b8b779)

  • Merge pull request #108 from NIDAP-Community/DESCRIPTION-update

Description update (be954aa)

  • Update DESCRIPTION

Signed-off-by: Ned Cauley <[email protected]> (e93caa7)

  • Merge pull request #106 from NIDAP-Community/dev

Dev (a221eda)

  • Merge pull request #105 from NIDAP-Community/DEG_fix

Changed default FDR method to BH (677d59e)

  • Changed default FDR method to BH (899e3f6)

  • Merge pull request #104 from NIDAP-Community/dev

Dev (1d470af)

  • Merge pull request #103 from NIDAP-Community/parameter_update

Added knit integration test markdowns (5bc88da)

  • Added knit integration test markdowns (046c413)

  • Merge pull request #102 from NIDAP-Community/dev

Dev (c7230f2)

  • Merge pull request #101 from NIDAP-Community/parameter_update

Fixed normalization test (35698a9)

  • Fixed normalization test (357227a)

  • Merge pull request #99 from NIDAP-Community/parameter_update

Parameter update (d22d061)

  • Updates to integration markdown tests for new study design parameters and normalization selection (5d37904)

  • Whole pipeline overview and modifications for paramater changes and multi-file normalization (168bc90)

  • Added additional boxplot to normalization test (585406d)

  • Merge pull request #96 from NIDAP-Community/studydesign

Studydesign (7de418b)

  • Added parameters for annotation fields, adjusted slide name to slide_name, added normalization plots (f93480d)

  • Added parameters for required annotation field names (66c1dfb)

  • Merge pull request #94 from NIDAP-Community/diffExpr_fix

Diff expr fix (7d398d1)

  • Add comments (317eda0)

  • Merge pull request #95 from NIDAP-Community/spatDeconv

update test and functions for spatDeconv, added published and relevant profile matrices to fixtures, expected image outputs to fixtures. (26907c8)

  • update test and functions (e68cd6f)

  • Remove extra file for diff exp testing (4058e2e)

  • Added more error messages in case region or group is missing (8cbf197)

  • Merge pull request #91 from NIDAP-Community/diffExpr

Diff expr (994635d)

  • changed Description file

Merge branch 'diffExpr' of https://github.com/NIDAP-Community/DSPWorkflow into diffExpr

Conflicts: DESCRIPTION R/differential_expression_analysis.R (47f8638)

  • Remove print statement (a5c35c3)

  • space (407f1d0)

  • space (11a1735)

  • Recommitting changes (624a8ff)

  • Merge pull request #90 from NIDAP-Community/dev

Synchronize diffExpr with dev (2668621)

  • Merge pull request #89 from NIDAP-Community/main

Synchronizing Dev to Main (7999c7e)

  • Added scientific notation and remove messages (4b352a1)

  • Update DESCRIPTION

Signed-off-by: Ned Cauley <[email protected]> (eb070e9)

  • Merge pull request #87 from NIDAP-Community/dev

Dev (cff2fee)

  • Update DESCRIPTION

Signed-off-by: Ned Cauley <[email protected]> (ac60309)

  • Updated nanostringnctools to 1.4.0 (7efef6f)

  • Updated DESCRIPTION to match resolved NIDAP environment DSP_pkg_testing (bd11104)

  • Merge pull request #83 from NIDAP-Community/dev

Updates for spatial decon vignette and version for NanostringNCTools (65446a4)

  • Updates for spatial decon vignette and version for NanostringNCTools (a1a21f5)

  • Merge pull request #82 from NIDAP-Community/dev

Dev (fecb39b)

  • Comma typo in DESCRIPTION (fcfdbec)

  • Update for R and Biobase version specifications (184b338)

  • Update gitflow-R-action.yml

Signed-off-by: Ned Cauley <[email protected]> (61981de)

  • Update gitflow-R-action.yml

Signed-off-by: Ned Cauley <[email protected]> (3e95fa1)

  • Asjusted version of gtable per build error on git action (14e3d89)

  • Corrected = to == (58f37f8)

  • Merge pull request #75 from NIDAP-Community/heatmap

Update heatmap.R (3b395e3)

  • Updates for resolving conda package build issues (ac570cd)

  • Update heatmap.R (797929f)

  • Update DESCRIPTION

Signed-off-by: Ned Cauley <[email protected]> (6a33e84)

  • Update DESCRIPTION

Signed-off-by: Ned Cauley <[email protected]> (7c6b4d2)

  • Merge pull request #74 from NIDAP-Community/dev

Updated for ggforce version and redocument (b5c8a12)

  • Updated for ggforce version and redocument (ff2a1e4)

  • Merge pull request #72 from NIDAP-Community/dev

Dev (33108a4)

  • Merge pull request #73 from NIDAP-Community/heatmap

changed internal calc.cv to .calcCv in Heatmap function (7b23f08)

Dev (6873033)

  • Merge pull request #70 from NIDAP-Community/spatDeconv2

modified spatDeconv helper (13a9ebc)

  • modified spatDeconv helper (b4261aa)

  • Merge pull request #69 from NIDAP-Community/diffexpr_fix

ttheme_default (ee4d318)

  • ttheme_default (cae3ff0)

  • Merge pull request #67 from NIDAP-Community/qcProc

Qc proc (a88347f)

  • add output table in return description (f302908)

  • Update gitflow-R-action.yml

Add new docker image

Signed-off-by: Ned Cauley <[email protected]> (016d89b)

  • qcProc clean warnings 1 (694fb61)

  • Merge pull request #65 from NIDAP-Community/Update_Github_Action

Update gitflow-R-action.yml (fb2a804)

  • Update gitflow-R-action.yml

Updated the Docker image version to use in action

Signed-off-by: ruiheesi <[email protected]> (3a7a118)

  • Merge pull request #64 from NIDAP-Community/GeoMxNorm

Updated for lowercamalcase (00d2098)

  • Merge pull request #63 from NIDAP-Community/Filtering

Updated for lowercamalcase (031e94e)

Diff expr (d1ef2fa)

  • Fixed merge conflicts for diff exp and dev (a787581)

  • Added skip on ci for NSCLC snapshot (92ac7b0)

  • Added skip on ci function for snapshot testing (f945185)

  • testing skipping snapshot testing on github ci (278529d)

  • fixed path on snap files (228786d)

  • Merge pull request #55 from NIDAP-Community/spatialDeconvolution

Spatial deconvolution (7fe5fc3)

  • Merge branch 'dev' into spatialDeconvolution

Signed-off-by: Ned Cauley <[email protected]> (0b140de)

  • Merge pull request #40 from NIDAP-Community/violinPlot

Violin plot (76e75a4)

  • Merge branch 'dev' into violinPlot

Signed-off-by: Ned Cauley <[email protected]> (31116fd)

Filtering (128cf85)

  • Merge branch 'dev' into Filtering

Signed-off-by: Ned Cauley <[email protected]> (99f2ac1)

  • NSCLC fixes for Filtering (8b7d22e)

  • Updates for NSCLC filtering (5e3b904)

  • Merge branch 'dev' into Filtering

Signed-off-by: Ned Cauley <[email protected]> (2afd535)

  • Updated diff exp helper for snap folder path (343ecaf)

  • Added check for max num of cores available (efd67a3)

  • Added placeholder files in downloaded fixtures folders (f5b0c42)

  • Error checking for dcc download, updates for test dataset parameters (95c2294)

  • Merge branch 'dev' of https://github.com/NIDAP-Community/DSPWorkflow into dev (2338d9a)

  • Updates to description file, mouse int test (7b2e447)

  • Merge pull request #48 from NIDAP-Community/DimReduct

fix aes inheritance for add.points (f825f74)

Signed-off-by: ChadAHighfill <[email protected]> (7ccb6e2)

Signed-off-by: Difei Wang <[email protected]> (4867331)

commit changes before merging (e376b2e)

Update syntax error (3e39d1e)

Conflicts: DESCRIPTION (4a0172f)

  • Updates to Description and deleted test files (143e624)

  • Merge pull request #38 from NIDAP-Community/dev

Changes for NIDAP integration: declare Biobase (3803ebc)

  • Merge pull request #37 from NIDAP-Community/diffExpr

Rewriting NAMESPACE (c77f99c)

  • Merge branch 'dev' into diffExpr

Signed-off-by: maggiecam <[email protected]> (7591a2b)

  • Make explicit call to Biobase package (795b82d)

  • Rewriting NAMESPACE (5e82792)

  • Merge pull request #36 from NIDAP-Community/diffExpr

Added Biobase::pData and changed gtable_add_rows parameter (1b2eae6)

  • Added Biobase::pData and changed gtable_add_rows parameter (d35b828)

  • Merge pull request #35 from NIDAP-Community/dev

Dev (6afdf67)

  • Merge branch 'main' into dev

Signed-off-by: Ned Cauley <[email protected]> (12cd549)

  • Merge pull request #34 from NIDAP-Community/dev_corrections

Dev corrections (d089b81)

  • added formatting to test result (0920b2f)

  • Removed duplicate mixedModelDE function call (6769922)

  • Updates to diff exp test snap paths (e65cddd)

  • changed format for test results for DEG, (ad3a161)

  • Merge branch 'dev_corrections' of https://github.com/NIDAP-Community/DSPWorkflow into dev_corrections (0528e29)

  • Corrected Kidney dcc file list and remade fixtures (4cc6aad)

  • merge conflict (e3af5e8)

  • Updated NAMESPACE and reintroduced changed to diff exp for stringr (179ebc0)

  • deleted old files (7220db8)

  • removed rmpfr from R scripts (b14c792)

  • Merge pull request #33 from NIDAP-Community/hotfix_3_28

Update DESCRIPTION and cleaned root directory (8ddd406)

  • Update DESCRIPTION and cleaned root directory (b3b9ae5)

  • Update DESCRIPTION to add magrittr and Update readme to use image in vignettes (b0eb7f7)

  • Merge pull request #32 from NIDAP-Community/dev

Dev (b30c557)

  • Merge pull request #31 from NIDAP-Community/diffExpr

Remove stringr from function - incompatible with r-4.1 (ad28d55)

  • Remove stringr from function - incompatible with r-4.1 (2755f31)

  • Merge pull request #30 from NIDAP-Community/integration_tests

Integration tests (7b29b5c)

  • Merge branch 'dev' into integration_tests

Signed-off-by: Ned Cauley <[email protected]> (0da610c)

Dev (e26a21c)

  • Update study_design.R

Signed-off-by: Ned Cauley <[email protected]> (6193584)

  • Update NAMESPACE

Signed-off-by: Ned Cauley <[email protected]> (91b50f0)

  • Merge pull request #28 from NIDAP-Community/dev

Dev (2f58092)

  • Merge pull request #27 from NIDAP-Community/StudyDesign

Study design (2234904)

  • Merge branch 'dev' into StudyDesign

Signed-off-by: Ned Cauley <[email protected]> (1f7abb4)

  • Merge pull request #26 from NIDAP-Community/integration_tests

Integration tests (2df4ee7)

  • Merge branch 'dev' into integration_tests

Signed-off-by: Ned Cauley <[email protected]> (1da7083)

  • Merge pull request #25 from NIDAP-Community/Filtering

Filtering (9a0ec30)

  • Merge pull request #24 from NIDAP-Community/GeoMxNorm

Geo mx norm (d621771)

  • Added comment (d2165c4)

  • Updated Kidney Integration test markdown (d729fbf)

  • Updated (1c84f14)

  • check (68d67ae)

  • Merge pull request #23 from NIDAP-Community/diffExpr

Set parameter pairwise = TRUE for default (6063c86)

  • Set parameter pairwise = TRUE for default (aaadd1b)

  • Updated error test (68707ba)

  • Check (c1ca228)

  • Check (984209d)

  • Check (cbdbfd9)

  • Initial changes to kidney integration test (80d7744)

  • Merge pull request #22 from NIDAP-Community/GeoMxNorm

Geo mx norm (621689e)

  • Merge pull request #21 from NIDAP-Community/Filtering

Filtering (206a249)

  • Updated organization of function, test, and helper scripts (41fa5ee)

  • Merge pull request #17 from NIDAP-Community/heatmap

Heatmap (65fb256)

  • Merge pull request #20 from NIDAP-Community/violinPlot

Violin plot (12c81ab)

  • Clean Up (c3964fa)

  • Merge branch 'dev' into violinPlot

Signed-off-by: Ned Cauley <[email protected]> (08ef6e3)

  • Merge pull request #19 from NIDAP-Community/SpatialDeconvolution

Spatial deconvolution (0c81890)

  • changed helper function (abb250c)

  • change helper function (ceff28c)

  • Updated organization of function, test, and helper scripts (304424f)

  • Updates to integration test, new PKC for NSCLC (b752559)

  • Updates (dc9149a)

  • Clean Up (fd4658e)

  • Clean Up (882f550)

  • Clean Up (fb7b641)

  • Merge pull request #12 from NIDAP-Community/DimReduct

Dim reduct (e1af0c2)

  • Updates (3a091a1)

  • Clean Up (037bcad)

  • dimReduct cleanup 1 (7e34989)

  • Merge pull request #10 from NIDAP-Community/QcProc

Qc proc (04fb8d9)

  • qcProc cleanup 4 (a89fb23)

  • Merge pull request #9 from NIDAP-Community/diffExpr

Differential Expression (68cc182)

  • Merge pull request #8 from NIDAP-Community/StudyDesign

Study design (7a0b592)

  • Updates (59ee6b4)

  • Update README.md

small edit

Signed-off-by: maggiecam <[email protected]> (3e7939b)

  • Update README.md

Added image

Signed-off-by: maggiecam <[email protected]> (ad8d86e)

  • Update README.md

Add image

Signed-off-by: maggiecam <[email protected]> (e3a363b)

  • Add files via upload

Signed-off-by: maggiecam <[email protected]> (b3ecda7)

  • Delete workflow_image.png

Signed-off-by: maggiecam <[email protected]> (83fe725)

  • Add files via upload

Added workflow image for readme

Signed-off-by: maggiecam <[email protected]> (9206949)

  • Update README.md

Describe Workflow

Signed-off-by: maggiecam <[email protected]> (7997822)

violinPlot branch is ahead by 9 commits (458a0d5)

merge DimReduct (25f4f14)

merge qcproc cleanup 1 (b4c93ec)

Study design (f9e9226)

  • Update to study design script (60522a7)

  • Cleaned Code (fad0b04)

  • Changed parameter names (fc83a0e)

  • test (ed8982a)

  • Update Check_On_Commit.yml

Signed-off-by: ruiheesi <[email protected]> (684d53b)

  • Update Check_on_Commit.sh

Signed-off-by: ruiheesi <[email protected]> (603950d)

Signed-off-by: ruiheesi <[email protected]> (cee97a2)

  • Merge branch 'main' into heatmap (b08d4fc)

  • test (f2c4d11)

  • Test branch (d90e4c5)

  • Update the lint checker to chekc if variable are in dotted case or lower case. Thus function name should alway produce warning as it shoudl eb lower camel. Line length limit is currently 120 (ef6380e)

  • Merge pull request #4 from NIDAP-Community/release_v0.1

Test Release v0.1 (217db3c)

  • Merge pull request #3 from NIDAP-Community/dev

Testing_merge to release actions (3be2756)

  • Merge pull request #2 from NIDAP-Community/feature_test

Update README.md (3d4e38d)

  • Update README.md

Signed-off-by: ruiheesi <[email protected]> (9a267f2)

  • Minor fix (3c17626)

  • Update github action to use docker image hosted on NIDAP-Community repo (4203a91)

  • Merge pull request #1 from ruiheesi/main

Add GitHub CI (96396d9)

  • Update actions files and file system structure (b251b00)

  • Merge branch 'NIDAP-Community:main' into main (3025db6)

  • Adding auto-generated files (113cf45)

  • Merge pull request #2 from ruiheesi/feature_test

Minor fix (0975bca)

Signed-off-by: ruiheesi <[email protected]> (58e9068)

  • Delete DSP_pkg_test_2_13.log

Signed-off-by: ruiheesi <[email protected]> (6b3036a)

merge unit test code (524e78c)

the commit.

push to git (f929806)

update local rep (2173b63)

merge (7766a30)

Conflicts: DESCRIPTION NAMESPACE (6631fc3)