Constructor api test reports - #86

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susansjy22 wants to merge 188 commits into

MangiolaLaboratory:constructor-APIfrom

susansjy22:constructor-API-test-reports

Commits on Jun 4, 2024

dummy
susansjy22
committed
5b880e5

Commits on Jul 15, 2024

update functions for anndata input work
myushen
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5029672

Commits on Jul 16, 2024

update module for anndata/sce input
myushen
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3b2e1d4

Commits on Jul 19, 2024

merge, solve conflicts from master
myushen
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6591188
fix
myushen
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09baa87

Commits on Jul 21, 2024

fix package dependency
myushen
committed
2d78027

Commits on Jul 23, 2024

fix mt-ribsome gene identification and pipeline running
myushen
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f2087a8

Commits on Jul 24, 2024

update emptydroplets
susansjy22
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94569aa
merge upstream
susansjy22
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049edb8
fix conflicts
susansjy22
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e2d50c4
Merge remote-tracking branch 'upstream/master' into modules_grammar_HPC
susansjy22
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41e86d2

Commits on Jul 29, 2024

fix
myushen
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ce36536

Commits on Jul 30, 2024

merge from master
myushen
committed
289a037

Commits on Jul 31, 2024

Merge remote-tracking branch 'upstream/master' into modules_grammar_HPC
susansjy22
committed
e635ab9
update testing
susansjy22
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ef267c7
clean readme
susansjy22
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51a9bf4

Commits on Aug 1, 2024

update run_target_pipeline() steps
susansjy22
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2d11c88

Commits on Aug 5, 2024

fix conflicts
myushen
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157d6dc
save transform assay in different formats
myushen
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e8c56ad

Commits on Aug 6, 2024

fix pipeline
myushen
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eff84af

Commits on Aug 7, 2024

update testing fibrosis
susansjy22
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49c045f

Commits on Aug 9, 2024

fix the pipeline for census anndata input
myushen
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f393990

Commits on Aug 14, 2024

testthat for census data
myushen
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3d6d946
update transformation function
myushen
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ef88d91

Commits on Aug 15, 2024

update transformation function
myushen
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44a9103
empty_droplet based on custom filter threshold
myushen
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29649e4
Merge branch 'custom_input_names' into transform-assays
myushen
authored
cd7de0e

Commits on Aug 19, 2024

update azimuth reference
myushen
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487359d

Commits on Aug 20, 2024

Merge branch 'azimuth_annotation' into transform-assays
myushen
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477ce36

Commits on Aug 21, 2024

test pilot data
myushen
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40f8bab
solve conflicts
myushen
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fc6019a

Commits on Aug 22, 2024

update azimuth reference
myushen
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12a2147

Commits on Aug 27, 2024

Merge pull request #78 from MangiolaLaboratory/constructor-API
stemangiola
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b234b3f

Commits on Aug 28, 2024

Update DESCRIPTION
stemangiola
authored
aa6f2a9
Update DESCRIPTION
stemangiola
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e75e881
update azimuth
myushen
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bcaacea
track files
stemangiola
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11e6118
version UP
stemangiola
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5112300

Commits on Aug 29, 2024

track files and solve conflicts.
myushen
committed
b6a616c
fix transform assay
stemangiola
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4e95796
add source argument to sutom functions
stemangiola
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37cd14e

Commits on Aug 30, 2024

deal with undefined targets
stemangiola
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fa632e5
fixed bug
stemangiola
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60a2815
still a bug with SCT filtering
stemangiola
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5d4ff7f
clean backend _target.R file
stemangiola
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442fa7f
fix transform_assay
myushen
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efcf63b

Commits on Sep 5, 2024

Update reports
susansjy22
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77c3ade
transform assays
susansjy22
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3713841
fix merge conflicts from construction-API
susansjy22
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9ad550c
loadPBMC
susansjy22
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4b69ff1
update testthat
myushen
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4eef896

Commits on Sep 17, 2024

fix fetching blueprint reference
myushen
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3dae5ef

Commits on Sep 24, 2024

update testthat
myushen
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aa858e5

Commits on Oct 1, 2024

update consensus function
stemangiola
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7d511a1
complete the consensus function
stemangiola
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b23f304
improve the consensus function
stemangiola
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792e2ca

Commits on Oct 4, 2024

Commits on Oct 7, 2024

fix consensus function
stemangiola
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2a00719
update exports
stemangiola
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1a183a6
pull
stemangiola
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4deffb7

Commits on Oct 14, 2024

Update report generation and testing
susansjy22
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df20eeb

Commits on Oct 23, 2024

mainly update cell consensus
stemangiola
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886c4a6

Commits on Oct 24, 2024

deal with undefined targets
stemangiola
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5cf02cb
fixed bug
stemangiola
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67714bf
still a bug with SCT filtering
stemangiola
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b6c6e2b
Merge branch 'drop-undefined-datasets' of https://github.com/MangiolaLaboratory/HPCell into drop-undefined-datasets
stemangiola
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3f45e07
update pipeline
myushen
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39d532d
Merge pull request #81 from MangiolaLaboratory/drop-undefined-datasets
stemangiola
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508b72f
merge master and solve conflicts
myushen
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285832e
Merge pull request #76 from myushen/transform-assays
stemangiola
authored
f7a2417

Commits on Oct 25, 2024

Merge pull request #82 from MangiolaLaboratory/custom_input_names
stemangiola
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c2afa9c
fix pipeline
stemangiola
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d5edd06
add man
stemangiola
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27632eb
add man
stemangiola
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44e27f1
pull
stemangiola
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eb074ed

Commits on Oct 26, 2024

update reports
susansjy22
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4d44610

Commits on Oct 30, 2024

update pipeline to work with HCA
stemangiola
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6332f9f

Commits on Nov 1, 2024

update functions
stemangiola
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df0f6d0
fix transform calculation
myushen
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082aa6e
fix
myushen
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0b23615
Merge pull request #83 from myushen/master
stemangiola
authored
eedc47b

Commits on Nov 4, 2024

fix temporary fix
stemangiola
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db97d74

Commits on Nov 13, 2024

typo
stemangiola
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8900f1b
Merge branch 'master' of github.com:Melbourne-COVID-Predict/jascap
stemangiola
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858f9d9
rename assay names for consistency
myushen
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f61b7aa

Commits on Nov 14, 2024

add idle time < inf
stemangiola
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6462999
do not skip if empty is null
stemangiola
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07ef147
typo
stemangiola
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fc51637
move step
stemangiola
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dfb080d
drop this filter, it does not make sense. The next steps can be robust
stemangiola
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67d29b6
Merge pull request #84 from myushen/master
stemangiola
authored
476f692

Commits on Nov 18, 2024

report tests passed
susansjy22
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7a03785
fix estimated counts in transform function
myushen
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34ff8f7
Merge branch 'master' of github.com:myushen/HPCell
myushen
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ac806de
fix
myushen
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2e4baf9
round estimated counts
myushen
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c8a3b1d

Commits on Nov 19, 2024

metacell module prototype
myushen
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bb5fd17

Commits on Nov 24, 2024

functional reports
susansjy22
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83fb26e

Commits on Nov 25, 2024

commit updated reports
susansjy22
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45409f8

Commits on Nov 26, 2024

updated reports FINAL
susansjy22
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cd173f5

Commits on Nov 28, 2024

remove duplicate package imports
bhuvad
committed
c95d5e1

Commits on Dec 3, 2024

Fix incorrect function imports
william-hutchison
committed
b6a0513

Commits on Dec 4, 2024

Fix incorrect remote address
william-hutchison
committed
0a5f924
Version up
william-hutchison
committed
7c06aae
Fix typo in code snippet
william-hutchison
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3d8b4e5
Version up
william-hutchison
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01c4d4e
Add SeuratDisk remote
william-hutchison
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4386e3d
Add NAMESPACE imports to DESCRIPTION
william-hutchison
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277878c

Commits on Dec 5, 2024

Update examples
william-hutchison
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0767c78
Version up
william-hutchison
committed
28731c2
Merge pull request #87 from william-hutchison/fix-installation
stemangiola
authored
81419ca

Commits on Dec 6, 2024

Commits on Dec 8, 2024

Merge branch 'MangiolaLaboratory:master' into master
myushen
authored
0dd37a4
update
myushen
committed
bc7add1

Commits on Dec 11, 2024

Fix incorrect variables passed to functions
william-hutchison
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410845d
Create SCT assay before attempting assignment
william-hutchison
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993e2b3
Prevent error when cell annotations are unavailable
william-hutchison
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9211c51
Remove NaN features from SCT assay
william-hutchison
committed
3880422
Version up
william-hutchison
committed
369d98b
Remove undefined function export
william-hutchison
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1cab853
Version up
william-hutchison
committed
3772e84

Commits on Dec 12, 2024

Stefano's changes made directly on Github
stemangiola
authored
ccd92d6

Commits on Dec 13, 2024

fix transform majority counts in estimation
myushen
committed
c7427aa

Commits on Dec 15, 2024

split metacell function
myushen
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6f96fcc

Commits on Dec 16, 2024

Added code to compute the mapping and added data required for mapping.
bhuvad
committed
fa5f150
solve single-column assay in sce object
myushen
committed
f1a495e

Commits on Dec 18, 2024

Commits on Jan 16, 2025

fix transform for missing cells issue
myushen
committed
494d9af

Commits on Jan 24, 2025

hpcell pseudobulk module accept saving to H5ad
myushen
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29c8517
Merge branch 'consensus_celltyping'
myushen
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bd895a7

Commits on Jan 29, 2025

cell type concensus module and pseudobulk
myushen
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40492c2
preprocess_simplify as a function not a module
myushen
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87c4268
fix
myushen
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0d83ea2

Commits on Jan 31, 2025

pseudobulk and concensus module dependency
myushen
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e50df95

Commits on Feb 6, 2025

metacell functions and unit tests
myushen
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550561e

Commits on Feb 10, 2025

replace NAs in annotations tibble to save anndata correctly
myushen
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53eaa6b
metacell module
myushen
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2ef018e
Merge branch 'MangiolaLaboratory:master' into metacell
myushen
authored
413f994
Merge branch 'metacell' of github.com:myushen/HPCell into metacell
myushen
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f3c19f7
Merge branch 'metacell' of github.com:myushen/HPCell into metacell
myushen
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f2f9316
Merge branch 'metacell' into master
myushen
authored
b7aed7c
Merge pull request #2 from myushen/master
myushen
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43522f5
Merge branch 'metacell' of github.com:myushen/HPCell into metacell
myushen
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aa476bb
merge the lastest cell-type-concensus function
myushen
committed
1b5e1e9

Commits on Feb 12, 2025

make metacell module work
myushen
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5d47cdb

Commits on Feb 13, 2025

fix metacell function error for large pipeline
myushen
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d85abbe

Commits on Mar 4, 2025

argument for users to choose mininum cells in metacell
myushen
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2f482ac

Commits on Mar 17, 2025

fix metacell module
myushen
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42db519

Commits on Mar 27, 2025

gamma documentation
myushen
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420cbf1

Commits on Mar 28, 2025

fix alive identification module
myushen
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d6249b7

Commits on Apr 1, 2025

cell chat module
myushen
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005efc4

Commits on Apr 7, 2025

append sample_id to cellchat tbl
myushen
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5b2fa70
Merge branch 'master' into cellchat
myushen
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e468cce
fix
myushen
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4773e50

Commits on Apr 8, 2025

update doublet_identification function and metacell dependencies
myushen
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72b87fb
fix
myushen
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432d0df

Commits on Apr 9, 2025

remove alive_tbl dependency in doublet function. force scDblFinder() work for small number of cells.
myushen
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eee248e

Commits on Apr 16, 2025

mark fail scdblfinder sample doublet to unknown
myushen
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9a75f50
Merge branch 'master' into cellchat
myushen
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9806985

Commits on Apr 30, 2025

Update report formatting
susansjy22
committed
23da4c7
add new reports remove old ones
susansjy22
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b1eb88d

Commits on May 8, 2025

skip cellchat object with only one celltype
myushen
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a70158f
delet old report rmd files
susansjy22
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3ecdfd6
Add empty droplet report qmd file
susansjy22
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da633fa

Commits on May 9, 2025

solve incorrect imported function
myushen
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746247b

Commits on May 15, 2025

change to use tar_quarto_raw(), and execute_param
susansjy22
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6d6132a
pull from upstream
susansjy22
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b129b62

Commits on Jun 9, 2025

universal cell type unified function, empty droplet percentage for rhasopdy tech
myushen
committed
0b88e97

Commits on Jun 12, 2025

adjust knn, npc for small number of cells in a sample
myushen
committed
969b460

Commits on Jun 16, 2025

redesign metacell for little sample cells. marks less than 3 single cells in a sample to metacell_2 = 1
myushen
committed
ab0e6d7

Commits on Jun 23, 2025

add communication weights/strength
myushen
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1f3d449

Commits on Jun 25, 2025

add pathway strength. remove thresh 0.05, return all communication, both insignificant and significant
myushen
committed
959337d

Commits on Jun 26, 2025

make feature_thresh as an input target in remove_empty_threshold module
myushen
committed
e738b1a

Commits on Jun 27, 2025

merge cellchat to master
myushen
committed
0284499

Commits on Jul 2, 2025

fix and cellchat mouse option
myushen
committed
540a2d9

Commits on Aug 13, 2025

dummy
susansjy22
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c13d850
pull updates from myushen/master
susansjy22
committed
37b160e
pull changes from remote
susansjy22
committed
5c3bf99

Commits on Aug 14, 2025

Update Utilities
susansjy22
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e552cc8
Fix pseudobulk to save the output
susansjy22
committed
564e515
Remove commented function
susansjy22
committed
efe6b61
Remove commented function
susansjy22
committed
fba80b3
Add ensembl_genes_biomart.rda
susansjy22
committed
daf6000