mcDETECT 2.0.0__py3-none-any.whl → 2.0.1__py3-none-any.whl

mcDETECT/__init__.py

@@ -1,3 +1,3 @@
-__version__ = "2.0.0"
+__version__ = "2.0.1"
 from .utils import *
 from .model import mcDETECT, spot_neuron, spot_granule, neighbor_granule, neuron_embedding_one_hot, neuron_embedding_spatial_weight

mcDETECT/model.py

@@ -11,7 +11,7 @@ from shapely.geometry import Point
 from sklearn.cluster import DBSCAN
 from sklearn.preprocessing import OneHotEncoder
 
-from utils import *
+from .utils import *
 
 
 class mcDETECT:

mcdetect-2.0.1.dist-info/METADATA

@@ -0,0 +1,40 @@
+Metadata-Version: 2.4
+Name: mcDETECT
+Version: 2.0.1
+Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
+Home-page: https://github.com/chen-yang-yuan/mcDETECT
+Author: Chenyang Yuan
+Author-email: chenyang.yuan@emory.edu
+Classifier: Programming Language :: Python :: 3
+Classifier: License :: OSI Approved :: MIT License
+Classifier: Operating System :: OS Independent
+Requires-Python: >=3.6
+Description-Content-Type: text/markdown
+License-File: LICENSE
+Requires-Dist: anndata
+Requires-Dist: miniball
+Requires-Dist: numpy
+Requires-Dist: pandas
+Requires-Dist: rtree
+Requires-Dist: scanpy
+Requires-Dist: scikit-learn
+Requires-Dist: scipy
+Requires-Dist: shapely
+Dynamic: author
+Dynamic: author-email
+Dynamic: classifier
+Dynamic: description
+Dynamic: description-content-type
+Dynamic: home-page
+Dynamic: license-file
+Dynamic: requires-dist
+Dynamic: requires-python
+Dynamic: summary
+
+# mcDETECT
+
+## Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
+
+#### Chenyang Yuan, Krupa Patel, Hongshun Shi, Hsiao-Lin V. Wang, Feng Wang, Ronghua Li, Yangping Li, Victor G. Corces, Hailing Shi, Sulagna Das, Jindan Yu, Peng Jin, Bing Yao* and Jian Hu*
+
+mcDETECT is a computational framework designed to study the dark transcriptome related to polarized compartments in brain using *in situ* spatial transcriptomics (iST) data. It begins by examining the subcellular distribution of mRNAs in an iST sample. Each mRNA molecule is treated as a distinct point with its own 3D spatial coordinates considering the thickness of the sample. Unlike many cell-type marker genes, which are typically found within the nucleus or soma, compartmentalized mRNAs often form small aggregates outside the soma. mcDETECT uses a density-based clustering approach to identify these extrasomatic aggregates. This involves calculating the Euclidean distance between mRNA points and defining the neighborhood of each point within a specified search radius. Points are then categorized as core points, border points, or noise points based on their reachability from neighboring points. mcDETECT recognizes each connected bundle of core and border points as a mRNA aggregate. To minimize false positives, it excludes aggregates that substantially overlap with somata, which are estimated by dilating the nuclear masks derived from DAPI staining. mcDETECT then repeats this process for multiple granule markers, merging aggregates from different markers that exhibit high spatial overlap. After aggregating across all markers, an additional filtering step removes aggregates containing mRNAs from negative control genes, which are known to be enriched exclusively in nuclei and somata. The remaining aggregates are considered individual RNA granules. mcDETECT then computes the minimum enclosing sphere for each aggregate to connect neighboring mRNA molecules from all measured genes and summarizes their counts, thereby defining the spatial transcriptome profile of individual RNA granules.

mcdetect-2.0.1.dist-info/RECORD

@@ -0,0 +1,8 @@
+mcDETECT/__init__.py,sha256=o9fQTRgcHPisSCcv0Cy-AtdiTSWrj-ITBK_FQxfnmKE,174
+mcDETECT/model.py,sha256=-r2_Ve0wxOALxiFk0REa58WjMea495yLZ6oXT-WWekw,28046
+mcDETECT/utils.py,sha256=kKw7KnrS-0llqtT32S_PDkag1jk4CWYkSm-FZeIJFAw,4510
+mcdetect-2.0.1.dist-info/licenses/LICENSE,sha256=uxq-shEWOGTIGVnQLmpElILmfCkuUhFZRAMnZUiKvtg,1070
+mcdetect-2.0.1.dist-info/METADATA,sha256=qMO7hrWgabHHp1_UxlDvsLmQYaBC7Nf85RPNxyBvA8o,3016
+mcdetect-2.0.1.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
+mcdetect-2.0.1.dist-info/top_level.txt,sha256=WwzBojt5U-T2hZ8llO6XgpM9OFIBkWQQldQKu19O8EY,9
+mcdetect-2.0.1.dist-info/RECORD,,

mcdetect-2.0.0.dist-info/METADATA

@@ -1,40 +0,0 @@
-Metadata-Version: 2.4
-Name: mcDETECT
-Version: 2.0.0
-Summary: Uncovering the dark transcriptome in polarized neuronal compartments with mcDETECT
-Home-page: https://github.com/chen-yang-yuan/mcDETECT
-Author: Chenyang Yuan
-Author-email: chenyang.yuan@emory.edu
-Classifier: Programming Language :: Python :: 3
-Classifier: License :: OSI Approved :: MIT License
-Classifier: Operating System :: OS Independent
-Requires-Python: >=3.6
-Description-Content-Type: text/markdown
-License-File: LICENSE
-Requires-Dist: anndata
-Requires-Dist: miniball
-Requires-Dist: numpy
-Requires-Dist: pandas
-Requires-Dist: rtree
-Requires-Dist: scanpy
-Requires-Dist: scikit-learn
-Requires-Dist: scipy
-Requires-Dist: shapely
-Dynamic: author
-Dynamic: author-email
-Dynamic: classifier
-Dynamic: description
-Dynamic: description-content-type
-Dynamic: home-page
-Dynamic: license-file
-Dynamic: requires-dist
-Dynamic: requires-python
-Dynamic: summary
-
-# mcDETECT
-
-## mcDETECT: Decoding 3D Spatial Synaptic Transcriptomes with Subcellular-Resolution Spatial Transcriptomics
-
-#### Chenyang Yuan, Krupa Patel, Hongshun Shi, Hsiao-Lin V. Wang, Feng Wang, Ronghua Li, Yangping Li, Victor G. Corces, Hailing Shi, Sulagna Das, Jindan Yu, Peng Jin, Bing Yao* and Jian Hu*
-
-mcDETECT is a computational framework designed to identify and profile individual synapses using *in situ* spatial transcriptomics (iST) data. It starts by examining the subcellular distribution of synaptic mRNAs in an iST sample. Unlike cell-type specific marker genes, which are typically found within nuclei, mRNAs of synaptic markers often form small aggregations outside the nuclei. mcDETECT uses a density-based clustering approach to identify these extranuclear aggregations. This involves calculating the Euclidean distance between mRNA points and defining the neighborhood of each point within a specified search radius. Points are then categorized into core points, border points, and noise points based on their reachability from neighboring points. mcDETECT recognizes each bundle of core and border points as a synaptic aggregation. To minimize false positives, it excludes aggregations that significantly overlap with nuclei identified by DAPI staining. Subsequently, mcDETECT repeats this process for multiple synaptic markers, merging aggregations from different markers with high overlaps. After encompassing all markers, an additional filtering step is performed to remove aggregations that contain mRNAs from negative control genes, which are known to be enriched only in nuclei. The remaining aggregations are considered individual synaptic aggregations. mcDETECT then uses the minimum enclosing sphere of each aggregation to gather all mRNA molecules and summarizes their counts for all measured genes to define the spatial transcriptome profile of individual synapses.

mcdetect-2.0.0.dist-info/RECORD

@@ -1,8 +0,0 @@
-mcDETECT/__init__.py,sha256=WaU6MqSrj7mF0VntYIJy2N0DNoZcnO_c7XGdt5JrLRc,174
-mcDETECT/model.py,sha256=5fMqJoirE1U2Cb7fd7bkPP5C8ofM1A5Tp5tKU7Rl5_A,28045
-mcDETECT/utils.py,sha256=kKw7KnrS-0llqtT32S_PDkag1jk4CWYkSm-FZeIJFAw,4510
-mcdetect-2.0.0.dist-info/licenses/LICENSE,sha256=uxq-shEWOGTIGVnQLmpElILmfCkuUhFZRAMnZUiKvtg,1070
-mcdetect-2.0.0.dist-info/METADATA,sha256=hUztmpphcWDcu2eoE294q6-QCKd_Oh5EmRAAyZk1ynk,2818
-mcdetect-2.0.0.dist-info/WHEEL,sha256=_zCd3N1l69ArxyTb8rzEoP9TpbYXkqRFSNOD5OuxnTs,91
-mcdetect-2.0.0.dist-info/top_level.txt,sha256=WwzBojt5U-T2hZ8llO6XgpM9OFIBkWQQldQKu19O8EY,9
-mcdetect-2.0.0.dist-info/RECORD,,