Ecosyste.ms: OpenCollective

An open API service for software projects hosted on Open Collective.

github.com/BioJulia/SingleCellProjections.jl

Analysis of Single Cell Expression data in Julia
https://github.com/BioJulia/SingleCellProjections.jl

Relax === to == in projection_isequal

Which fixes a bug that can occur when serializing models.

34a581deb868fefbadbb8467e6b21e376eec14cc authored 10 months ago by Rasmus Henningsson <[email protected]>
Patch bump, update CHANGELOG

b2a95668f010e8dbd28fb74fa8b0f085642fb3b0 authored 11 months ago by Rasmus Henningsson <[email protected]>
Add seed kwarg to svd/force_layout/pma

NB: using `seed` requires StableRNGs to be loaded.

9cf172cf549f8ee3aff906f934ea17903ed3f608 authored 11 months ago by Rasmus Henningsson <[email protected]>
Patch bump, update CHANGELOG

d645768ff953b6d44df3a1dbc93184bd1131f13b authored about 1 year ago by Rasmus Henningsson <[email protected]>
load_counts now handles single sample

* `load_counts` now works properly when passing a single filename (as a
string or a vector with ...

e924167656f7e663e4e6c20b0a9b44ee83daec78 authored about 1 year ago by Rasmus Henningsson <[email protected]>
Local Outlier Factor (#15)

Local Outlier Factor

Implementation of Local Outlier Factor (LOF).
Nearest neighbors can be ...

5e23d9269ad1ccd65de418e9fe8dd9b24207dc2d authored about 1 year ago by Rasmus Henningsson <[email protected]>
Fix docstring for project(data, models)

9de4ecdd440614a03a7c552281114112eafe4532 authored about 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump. Update CHANGELOG.

b23a91e3620bb885488efec7d6116f293384292d authored about 1 year ago by Rasmus Henningsson <[email protected]>
Unit test pseudobulk projections

0de00ebfc26f61583197425dc62127049ddef693 authored about 1 year ago by Rasmus Henningsson <[email protected]>
pseudobulk unit tests and bug fixes

a96cfec0b9b7d7c534456c8260baaebc72a7547c authored about 1 year ago by Rasmus Henningsson <[email protected]>
pseudobulk implementation

46af98fb9070df325b7405930b638bdeed84c737 authored about 1 year ago by Rasmus Henningsson <[email protected]>
compat for stdlibs

de29d2f1a7756337260fb277039b3da516020153 authored about 1 year ago by Rasmus Henningsson <[email protected]>
Fix typo in tutorial.md (#11)

build -> built

e7384906085bf9fd8c5ea7ff0c72ce18687cd26c authored over 1 year ago by Michael Persico <[email protected]>
HDF5 v0.17 compat, bump patch version

18adcb77df6d7d84fc7293cb3e1360242d005991 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump, SingleCell10x compat

b986a4f2f0c03ebebcd0c8b3117788beae8206f9 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test PrincipalMomentAnalysis extension

35f462d584a3bdf113d3fbb8fefd56fa49c8b06c authored over 1 year ago by Rasmus Henningsson <[email protected]>
Package extensions (#9)

Migration from Requires.jl to Package Extensions.

Follows the description from:
https://pkgd...

66e2e7358336ff93af7b0212b379fe69c4d453f0 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add badge for stable docs

90d692e62206bb1859dcd5d2572fc47b2faf6c62 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Update doc links after repo move

182399028ee496b777b668f2f249a378f0413bf3 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Update README.md (#8)

27ed5541d551dae23057845b7e25c24f44d486c2 authored over 1 year ago by Kevin Bonham <[email protected]>
Add SCTransformModel missing method, patch bump

b69d7c77403b7f971ae0dd07b18daea56cb52a83 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Add precompile statements

* sctransform (Float32)
* logtransform (Float64, Float32)
* tf_idf_transform (Float64, Float32)
...

14c8da25aa1244593b2933755969848f4a0ece16 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Update CHANGELOG

ceb43b935da86a113e380adb8fba5b13fbfed6e3 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

e999682c67142523f847a69d7acf85a2394d1f91 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Allow CI nightly failures. Fix CI badge.

7037814f66d0fca891f0f14bb67a94e35d06e4ac authored over 1 year ago by Rasmus Henningsson <[email protected]>
Float32 support (#6)

Support for specifying eltype of the transformed sparse matrix (for sctransform, logtransform an...

c25baf89a7e7f55ac4ab060f02d697dd0a6b0b09 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Clarify that logtransform uses base 2

7eb88817430f834810d9546e42bf23016a3c3064 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Run CI on latest Julia (1.9)

faa30921dc599838215ef8ef82b1b1432d08eb2a authored over 1 year ago by Rasmus Henningsson <[email protected]>
Move some common test code to test_utils

db7061a14782ac91c6f66802111ae8003cb5e480 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test F-test (categorical) without intercept

a9ee261fcf17e57a6237c9234b9be0e5c42fdeb6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test tests without intercept

b386b9e69a818d10132e6ad940033662127346da authored over 1 year ago by Rasmus Henningsson <[email protected]>
docstring danger->note since we now throw error

d80c195a6147a0c0620265159834b865a431913a authored over 1 year ago by Rasmus Henningsson <[email protected]>
Set version 0.3

ed6f3e573f795805e68df2801199dc81a7ef37fe authored over 1 year ago by Rasmus Henningsson <[email protected]>
Update CHANGELOG

e504980fe90468591ef4d9bd17159720203fe1b6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Throw error if ftest/ttest-ing a Normalized Datamatrix

d3923de73b1c6087089ca7d1d5cad21f84bbc585 authored over 1 year ago by Rasmus Henningsson <[email protected]>
logtransform and tf_idf_transform now filters to Gene Expression features by default

a4c4e4eeadef8080c999962658fcb8a4a9c8ce69 authored over 1 year ago by Rasmus Henningsson <[email protected]>
groupA/B to group_a/b

c4d18f6824ebc5e036b5436a0e9a084b0a4fb3c7 authored over 1 year ago by Rasmus Henningsson <[email protected]>
More covariate unit testing

9e8d31518dbc63192054886b03cf4f3d2b39403f authored over 1 year ago by Rasmus Henningsson <[email protected]>
mannwhitney covariate refactoring

5cccc3dfc2584e76398687c389143202d58ede3f authored over 1 year ago by Rasmus Henningsson <[email protected]>
ftest/ttest covariate refactoring

Convert strings to CovariateDesc as soon as possible to avoid duplicate code paths.

b24b206acaf1079d862fe8dec2a7edf721838b66 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Two-Group A vs B fix. More ttest!, ttest docstrings.

7e4a1f4ab66b48d427040577cc33ad4a0c3560c7 authored over 1 year ago by Rasmus Henningsson <[email protected]>
start writing t-test docstring

a4efa27c8ccbf027f4fb47da90cf5480f8f5a79c authored over 1 year ago by Rasmus Henningsson <[email protected]>
ftest docstring

Improve ftest_table docstring and add docstrings for ftest! and ftest.

2f33d4c80a77e9706488f310927fc5890856064c authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix TwoGroup centering, add ftest_table docstring

b9b7827f4323bcff3e9c3cbb7ffaeafe73fd969d authored over 1 year ago by Rasmus Henningsson <[email protected]>
More thorough MannWhitney unit tests

4030c26244c34247e123f728cd1ca89759d3126a authored over 1 year ago by Rasmus Henningsson <[email protected]>
mannwhitney now supports h1_missing kwarg

8a689c3e1f7e6d8076fa63f3661b491d15ae7873 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Compute difference for ttests

59aedfa225fd1ec8c654ab41cf8161dc625e8317 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Use keepachangelog.com-style changelogs

11388deb9b1d7779bdb33af698c990e44412710c authored over 1 year ago by Rasmus Henningsson <[email protected]>
Unit test twogroup covariate in normalize_matrix

9a28d61c2baf45eaa105b124e791e9da4e8513a6 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Two-Group support in ttest / covariates

fefa64ab3a3a57362cebe2c4d5cbcb1769e53f66 authored over 1 year ago by Rasmus Henningsson <[email protected]>
h1_missing and h0_missing kwargs

bad603f7eeb0cf58580476e4082dcc2d5cd9e1ac authored over 1 year ago by Rasmus Henningsson <[email protected]>
Remove deprecated differentialexpression

NB: Breaking change.
Use other tests instead.

9753dcb358571c2787549ca25a7cc88f31f6c2a8 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Missing values not allowed in categorical covariates

NB: Breaking change.

211db41756dadd0ad3f3aec118f9ec685cf25690 authored over 1 year ago by Rasmus Henningsson <[email protected]>
renamed test->h1, null->h0

c1828537d36a9a7d2a3d9c17b978fc2d08296c15 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Test output cols can now be nothing. More unit tests.

9cc347919d6c2a26fd030daff8a8eaab74c9b97f authored over 1 year ago by Rasmus Henningsson <[email protected]>
ftest!, ftest, ttest!, ttest

104f3e7621e20cf0e4c88595e9225d2e98ef592d authored over 1 year ago by Rasmus Henningsson <[email protected]>
ttest_table and some changes to share code with ftest

0efdfd5c07d8ccd4e592ab8b0935563921bc92d1 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Avoid SVD for single column

7f12c6a62078c0391c349ce7b0c3f20ca07f5293 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Fix F-test edge cases, prepare for t-test

4c9e731f35c9795e0f1ffd39dc242c889acf7004 authored over 1 year ago by Rasmus Henningsson <[email protected]>
ftest_table: null model is now kwarg)

a17c7d43af62abeda8bfbc3c93f41a96906d8014 authored over 1 year ago by Rasmus Henningsson <[email protected]>
FTest unit tests

a1dc15024a7cbc35cafbcbf69beb64824ea43fcf authored over 1 year ago by Rasmus Henningsson <[email protected]>
Initial FTest unit tests

3e00d1eef1bacb4172efec2c6d8dc9862e883e00 authored over 1 year ago by Rasmus Henningsson <[email protected]>
renamed MannWhitnet unit tests file

203e441e4ed8d89e96ac26bcb657cf9640f62a52 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Minor ftest fixes

335881327846ca21221e34a63a0033a87706f2fc authored over 1 year ago by Rasmus Henningsson <[email protected]>
WIP ftest

7fed3acd8247fbb1fdf4a3603684e7eab1cc6a38 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Mann-Whitney U test (Wilcoxon rank-sum test) (#4)

Mann-Whitney U test, also known as Wilcoxon rank-sum test.

* Threaded implementation
* DataM...

267cd33dfa2c534e4ff31ce3f3da19d9846ef9e0 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

6ddbd4cf887c5dd05090944e95a31fdf2bf4b7d1 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Rename std to scaling

The output from normalize_matrix with scale=true and annotate=true is
now correctly called scali...

b1527e742c98977ee9790788c054411feb85be50 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

1d143b1c5da2892d27435c0c2521aeabb216aed4 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Migrate from SnoopPrecompile to PrecompileTools (#3)

b742c27f6a48817bf3f5b1ebd906738944bfe187 authored over 1 year ago by Tim Holy <[email protected]>
copy(::MatrixExpression)

Implement copy(::MatrixExpression).
Copies the structure, but not the matrices (leaves).

69d5d0c358b48803fbd53bb212d006862fe74f4f authored over 1 year ago by Rasmus Henningsson <[email protected]>
copy(::DataMatrix)

With kwargs for fine-grained control.

005456c14cdf13b8771107d9a0d1ae863e8f0899 authored over 1 year ago by Rasmus Henningsson <[email protected]>
ID col setters and safety

Add `set_var_id_cols!` and `set_obs_id_cols!` for updating ID cols with
checks that they are val...

f58ab1c2a92bcd831148a53377d7ca3cb6ca4c55 authored over 1 year ago by Rasmus Henningsson <[email protected]>
Patch bump

0a4d845dcf06ae6939b4545619ff6aaedb2f4dae authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix docs for umap and tsne

12c4172d40cc458ca80cae5424c37766daec4621 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix <details> html block

c29aecd09f834369a773a68cf829dcfc07777bd0 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Tutorial now runs code to get better output

The tutorial now runs a (faked) analysis. Benefits:
* Changes `show` methods will now be reflect...

50800d6ce00047f6b019619f6c786824b1c514fa authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix NaN issue with zero singular values

926b1d46a219e1198e506279e5030c302d463534 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix typo in @info

c912af225548fdb30386126eaada7bdde18131b1 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Remove tutorial from README

...and refer to the tutorial in the docs

447190931571531816ae4a65601aaac9b8b5e29d authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Update plots in tutorial/README

e6a64f417e0fb06889f346edf9843c0efb1f0751 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Installation instructions and Tutorial

aff442c1517e4d076a37ced42d2e95b1709efc7f authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Add intro text

c4ff5361060d662f79d6794c03487bbfb625ee0a authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Read-only clarifications

e9ea3bbfecdb86dd949227ee0a8c960e203fbf19 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
DataMatrix docs

ec6e7249d5f68a2bd48cc15613a323858e1321a6 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
var_to_obs_table unit test

ea2b0ecc19d454146d2fcad47c086d75d1a7cb26 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit test var_to_obs projection

c07bad8db9394635324f660aaa92831c756e5e3d authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix eltype of columns produced by var_to_obs

b8197189858ce27b43d6f098e8a7483db03aca65 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
var_to_obs improvements and unit tests

* Renamed `out_names` kwarg to `names`.
* Introduced `name_src` kwarg for convenient naming by o...

2cf223e398a807f48aedf617411d2254071fa253 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
unit test sctransform var_filter==nothing

902ffa2b90b74c67a57d18c34576bae211badee4 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
tf-idf unit testing

89b6532ce4657b3637f90509f5d5655b636663e7 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix tf-idf projection reordering bug

deef0f6d1b6da81472765150cb7145a88cb80e8d authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit testing

* tf-idf transform
* fix show unit test bug
* disable umap projection testing for now (numerical...

12d2be3efeb5bd21a99ef56bc4d751c85cb1fc59 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit test filter projection

1b3e177e059f3fa97d8b2066e1af3a35402aec62 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit testing projection of normalization of raw counts

55671b5270922f18744858e985d6b217baff9530 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit test logtransform projections with gene subsets

7fdf65d47a78a3e83edc449ac315554685eadeab authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit test missing value reconstruction

7c36eff3fe36e27a03f5b20730981b2a6602242f authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Unit test projections with different set of variables

f42fa22634024a77f4fad90e51cdfa099e580460 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Fix projection unit test

f2e0636558ab06d08bb4a26e6a26d5ef440eaa15 authored almost 2 years ago by Rasmus Henningsson <[email protected]>
Update installation instructions

f558104a72629287e5412f5779336be644e70a98 authored almost 2 years ago by Rasmus Henningsson <[email protected]>