popV version: 0.6.0

OnClass.data-00000-of-00001

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ed9b48fb9a606e6a08bccc9e911f08ad543702d81f7e281378ef1a434850eab8
+oid sha256:c7d7b27a347598a59e82ff7137cb77157daaa082e07e4f3b755c7d7c19222f42
 size 27239224

OnClass.npz

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:c3ef7e6b4e5dfc0c81b8660421772539738b5bdf243cf9e883e8035fd5152bad
-size 144112694
+oid sha256:b70e36ecee04f773a507f79263adf8f98ef55bb3e2d6a3f5918b4177e20ccd04
+size 144112689

README.md

@@ -1,56 +0,0 @@
----
-library_name: popV
-license: cc-by-4.0
-tags:
-- biology
-- genomics
-- single-cell
-- AnnData:0.12.2
-- scikit_learn:1.7.2
-- organism:Homo sapiens
-- Python:3.12.8
-- popV:0.6.0
-- 'tissue: diverse'
----
-
-Popular Vote (popV) model for automated cell type annotation of single-cell RNA-seq data. We provide here pretrained models
-for plug-in use in your own analysis.
-Follow our [tutorial](https://github.com/YosefLab/popV/blob/main/tabula_sapiens_tutorial.ipynb) to learn how to use the model for cell type annotation.
-
-# Model description
-
-Tabula Sapiens is a benchmark, first-draft human cell atlas of over 1.1M cells from 28 organs of 24 normal human subjects. This work is the product of the Tabula Sapiens Consortium. Taking the organs from the same individual controls for genetic background, age, environment, and epigenetic effects, and allows detailed analysis and comparison of cell types that are shared between tissues.
-
-**Link to CELLxGENE**:
-Link to the [data](https://cellxgene.cziscience.com/e/b806712d-18b0-454c-a0fe-9909159e07c7.cxg/) in the CELLxGENE browser for interactive exploration of the data and download of the source data.
-
-**Training Code URL**:
-Not provided by uploader.
-
-# Metrics
-
-We provide here accuracies for each of the experts and the ensemble model. The validation set accuracies are
-computed on a 10% random subset of the data that was not used for training.
-
-| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
-| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| spermatid | 402 | 0.98 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 1.00 | 0.98 | 1.00 |
-| spermatocyte | 308 | 0.97 | 0.98 | 0.98 | 0.97 | 0.00 | 0.97 | 0.99 | 0.96 | 0.99 |
-| male germ cell | 8 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |
-| spermatogonium | 9 | 0.80 | 0.71 | 0.62 | 0.62 | 0.00 | 0.75 | 0.84 | 0.63 | 0.71 |
-
-The train accuracies are computed on the training data.
-
-| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |
-| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |
-| spermatid | 3607 | 0.98 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |
-| spermatocyte | 2762 | 0.97 | 0.99 | 0.99 | 0.98 | 0.00 | 0.97 | 0.98 | 0.97 | 0.99 |
-| male germ cell | 108 | 0.95 | 0.99 | 0.96 | 0.96 | 0.00 | 0.96 | 1.00 | 0.98 | 0.99 |
-| spermatogonium | 55 | 0.80 | 0.95 | 0.83 | 0.87 | 0.00 | 0.81 | 0.96 | 0.87 | 0.94 |
-
-</details>
-
-
-# References
-
-Tabula Sapiens reveals transcription factor expression, senescence effects, and sex-specific features in cell types from 28 human organs and tissues, The Tabula Sapiens Consortium; bioRxiv, doi: https://doi.org/10.1101/2024.12.03.626516

accuracies.json

@@ -1,4 +1,4 @@
 {
-    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| spermatid | 402 | 0.98 | 0.99 | 0.99 | 0.98 | 0.00 | 0.98 | 1.00 | 0.98 | 1.00 |\n| spermatocyte | 308 | 0.97 | 0.98 | 0.98 | 0.97 | 0.00 | 0.97 | 0.99 | 0.96 | 0.99 |\n| male germ cell | 8 | 1.00 | 1.00 | 1.00 | 1.00 | 0.00 | 1.00 | 1.00 | 1.00 | 1.00 |\n| spermatogonium | 9 | 0.80 | 0.71 | 0.62 | 0.62 | 0.00 | 0.75 | 0.84 | 0.63 | 0.71 |",
-    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| spermatid | 3607 | 0.98 | 0.99 | 0.99 | 0.99 | 0.00 | 0.98 | 0.99 | 0.98 | 0.99 |\n| spermatocyte | 2762 | 0.97 | 0.99 | 0.99 | 0.98 | 0.00 | 0.97 | 0.98 | 0.97 | 0.99 |\n| male germ cell | 108 | 0.95 | 0.99 | 0.96 | 0.96 | 0.00 | 0.96 | 1.00 | 0.98 | 0.99 |\n| spermatogonium | 55 | 0.80 | 0.95 | 0.83 | 0.87 | 0.00 | 0.81 | 0.96 | 0.87 | 0.94 |"
+    "query_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| spermatid | 389 | 0.98 | 0.98 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.97 | 0.99 |\n| spermatocyte | 319 | 0.97 | 0.97 | 0.98 | 0.98 | 0.00 | 0.97 | 0.98 | 0.96 | 0.98 |\n| male germ cell | 10 | 0.95 | 0.95 | 0.87 | 0.95 | 0.00 | 0.83 | 1.00 | 0.95 | 0.91 |\n| spermatogonium | 9 | 0.80 | 0.82 | 0.67 | 0.75 | 0.00 | 0.57 | 0.82 | 0.70 | 0.82 |",
+    "ref_accuracy": "| Cell Type | N cells |  celltypist |  knn bbknn |  knn harmony |  knn on scvi |  onclass |  scanvi |  svm |  xgboost | Consensus Prediction |\n| --- | --- | --- | --- | --- | --- | --- | --- | --- | --- | --- |\n| spermatid | 3620 | 0.98 | 0.99 | 0.99 | 0.99 | 0.00 | 0.99 | 0.99 | 0.98 | 0.99 |\n| spermatocyte | 2751 | 0.98 | 0.99 | 0.98 | 0.98 | 0.00 | 0.98 | 0.98 | 0.97 | 0.99 |\n| male germ cell | 106 | 0.97 | 0.99 | 0.97 | 0.98 | 0.00 | 0.93 | 1.00 | 1.00 | 0.99 |\n| spermatogonium | 55 | 0.85 | 0.91 | 0.82 | 0.85 | 0.00 | 0.78 | 0.96 | 0.90 | 0.92 |"
 }

celltypist.pkl

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:d15b82f674958a66ffd81b62921ff89404679dc6d0ad4dac6c30c1546b9013b6
+oid sha256:f428e8da4c3cc59267f6ac9fbb290c80645e8867171ba3cf679d6cf4e8c52264
 size 233270

faiss_index.index

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:382bf8e8e7f416cc8f1c98e188486c2e4669708139123a79e53d28281cd4df94
+oid sha256:d8f59bb0a8960a919af1c502266db4473de09a2c9a43e1ca46e38eacbff22c3a
 size 1309645

harmony_knn_classifier.index

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:756c1658e18b8370d0d69f312382406c2f6dc0472ebbcb690e15658f92c8bbda
+oid sha256:1059357c965d1ba044057ca2b84f2f29cd6fff982aba09b4eb262bd9c702f5c4
 size 1306445

metadata.json

@@ -1,33 +0,0 @@
-{
-    "popv_version": "0.6.0",
-    "anndata_version": "0.12.2",
-    "scikit_learn_version": "1.7.2",
-    "setup_dict": {
-        "ref_labels_key": "popv_labels",
-        "ref_batch_key": "batch_key",
-        "unknown_celltype_label": "unassigned"
-    },
-    "prediction_keys": [
-        "popv_celltypist_prediction",
-        "popv_knn_bbknn_prediction",
-        "popv_knn_harmony_prediction",
-        "popv_knn_on_scvi_prediction",
-        "popv_onclass_prediction",
-        "popv_scanvi_prediction",
-        "popv_svm_prediction",
-        "popv_xgboost_prediction"
-    ],
-    "method_kwargs": {},
-    "methods": [
-        "CELLTYPIST",
-        "KNN_BBKNN",
-        "KNN_HARMONY",
-        "KNN_SCVI",
-        "ONCLASS",
-        "SCANVI_POPV",
-        "Support_Vector",
-        "XGboost"
-    ],
-    "cellxgene_url": "https://cellxgene.cziscience.com/e/b806712d-18b0-454c-a0fe-9909159e07c7.cxg/",
-    "organism": "Homo sapiens"
-}

minified_ref_adata.h5ad

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8fd5e846f6189ed84a901082acb53e7bc6fd55806c38bc04e6c04e39ee1bc927
-size 18859164

pynndescent_index.joblib

@@ -1,3 +0,0 @@
-version https://git-lfs.github.com/spec/v1
-oid sha256:8fdb6eee18d2def4333b46bcff537e0759bc814efcd5613767182939946764b1
-size 5358348

scanvi/model.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:7eb7ab9edaf3285ea4b8c327c107e619680cc2ca08b3a6d910d60ab47131a4a3
+oid sha256:a2f59956af272469870211b96d91a29056bddb53854479b80e2bf4bf2979ece6
 size 11344629

scvi/model.pt

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:41d7b6317e3de2d58d565cd29da89daea81c849a74e5113006d2c2ae97f0c1f6
+oid sha256:f2740f8fadf16587fe4d5327490867f31b79e8be3985cfbd84f0b159714dccf9
 size 10828742

scvi_knn_classifier.index

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:1f7b5dd9e32d33ef28477b204c26fb040f242f58ac59292219db1c96a8252693
+oid sha256:39bc933391075b16061cd9dae766092faaa83bfb481b7a7ba78cdc6841b63946
 size 522605

svm_classifier.joblib

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:ea6c2c28aa260c28f4b50690a00016108a1c97e67d719ed26d63bfe4f7234fea
+oid sha256:4c46db8ad4f5b0bf5014c4a0701b2d7195b3fe190ef18fabad6ac897197aa7b5
 size 65376

xgboost_classifier.model

@@ -1,3 +1,3 @@
 version https://git-lfs.github.com/spec/v1
-oid sha256:a4570c2dd0bd2d060bc854fb8cfb5ce04549f678d45cfdbdd5231ba4fa68b8ba
-size 939455
+oid sha256:29cb4202398024f165cd1973110a8c3007e4808c337ef7df7ef46fbe57103fa4
+size 927074