Succinct Representation of Single Cells

Navigation

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ZengFLab from gravatar.com ZengFLab

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: MIT License
  • Author: Feng Zeng
  • Requires: Python >=3.10
Classifiers
Report project as malware

Project description

SURE: SUccinct REpresentation of cells

SURE introduces a vector quantization-based probabilistic generative model for calling metacells and use them as landmarks that form a coordinate system for cell ID. Analyzing single-cell omics data in a manner analogous to reference genome-based genomic analysis.

$$\color{red}\text{\textbf{UPDATE}}$$

An update has been distributed. Users can access to it via SUREv2. It provides Python classes that users can call SURE in scripts. It also provide the command that users can run SURE in the shell. Additionally, SUREv2 supports the calling of metacells for multi-omics datasets.

Installation

  1. Create a virtual environment
conda create -n SUREv1 python=3.10 scipy numpy pandas scikit-learn && conda activate SUREv1
  1. Install PyTorch following the official instruction.
pip3 install torch torchvision --index-url https://download.pytorch.org/whl/cu126
  1. Install SURE
pip3 install SURE-tools

Example 1: Calling metacells for a single-cell dataset

Users can refer to here for details.

Example 2: The hierarchical assembly of large-scale dataset(s)

Users can refer to here for details.

Example 3: Human brain cell atlas

Users can refer to here for details.

Example 4: Metacell calling for scATAC-seq data

Users can refer to here for details.

Project details

Verified details

These details have been verified by PyPI
Maintainers
Avatar for ZengFLab from gravatar.com ZengFLab

Unverified details

These details have not been verified by PyPI
Project links
Meta
  • License: MIT License
  • Author: Feng Zeng
  • Requires: Python >=3.10
Classifiers

Release history Release notifications | RSS feed

4.8.9

4.8.8

4.8.7

4.8.6

4.8.5

4.8.4

4.8.3

4.8.2

4.8.1

4.8.0

4.7.8

4.7.7

4.7.6

4.7.5

4.7.4

4.7.3

4.7.2

4.7.1

4.7.0

4.6.10

4.6.9

4.6.8

4.6.7

4.6.6

4.6.5

4.6.4

4.6.3

4.6.2

4.6.1

4.6.0

4.5.18

4.5.17

4.5.16

4.5.15

4.5.14

4.5.13

4.5.12

4.5.11

4.5.10

4.5.9

4.5.8

4.5.7

4.5.6

4.5.5

4.5.4

4.5.3

4.5.2

4.5.1

4.5.0

4.4.10

4.4.9

4.4.8

4.4.7

4.4.6

4.4.5

4.4.4

4.4.3

4.4.2

4.4.1

4.4.0

4.3.0

4.2.6

4.2.5

4.2.4

4.2.3

4.2.2

4.2.1

4.2.0

4.1.1

4.1.0

4.0.30

4.0.29

4.0.28

4.0.27

4.0.26

4.0.25

4.0.24

4.0.23

4.0.22

4.0.21

4.0.20

4.0.19

4.0.18

4.0.17

4.0.16

4.0.15

4.0.14

4.0.13

4.0.12

4.0.11

4.0.10

4.0.9

4.0.8

4.0.7

4.0.6

4.0.5

4.0.4

4.0.3

4.0.2

4.0.1

4.0.0

3.7.4

3.7.3

3.7.2

3.7.1

3.7.0

3.6.14

3.6.13

3.6.12

3.6.11

3.6.10

3.6.9

3.6.8

3.6.7

3.6.6

3.6.5

3.6.4

3.6.3

3.6.2

3.6.1

3.6.0

3.5.27

3.5.26

3.5.25

3.5.24

3.5.23

3.5.22

3.5.21

3.5.20

3.5.19

3.5.18

3.5.17

3.5.16

3.5.15

3.5.14

3.5.13

3.5.12

3.5.11

3.5.10

3.5.9

3.5.8

3.5.7

3.5.6

3.5.5

3.5.4

3.5.3

3.5.2

3.5.1

3.5.0

3.4.29

3.4.28

3.4.27

3.4.26

3.4.25

3.4.24

3.4.23

3.4.22

3.4.21

3.4.20

3.4.19

3.4.18

3.4.17

3.4.16

3.4.15

3.4.14

3.4.13

3.4.12

3.4.10

3.4.9

3.4.8

3.4.7

3.4.6

3.4.5

3.4.4

3.4.3

3.4.2

3.4.1

3.4.0

3.3.37

3.3.36

3.3.35

3.3.34

3.3.33

3.3.32

3.3.31

3.3.30

3.3.29

3.3.28

3.3.27

3.3.26

3.3.25

3.3.24

3.3.23

3.3.22

3.3.21

3.3.20

3.3.19

3.3.18

3.3.17

3.3.16

3.3.15

3.3.14

3.3.13

3.3.12

3.3.11

3.3.10

3.3.9

3.3.8

3.3.7

3.3.6

3.3.5

3.3.4

3.3.3

3.3.2

3.3.1

3.3.0

3.2.41

3.2.40

3.2.39

3.2.38

3.2.37

3.2.36

3.2.35

3.2.34

3.2.33

3.2.32

3.2.31

3.2.30

3.2.29

3.2.28

3.2.27

3.2.26

3.2.25

3.2.24

3.2.23

3.2.22

3.2.21

3.2.20

3.2.19

3.2.18

3.2.17

3.2.16

3.2.15

3.2.14

3.2.13

3.2.12

3.2.11

3.2.10

3.2.9

3.2.8

3.2.7

3.2.6

3.2.5

3.2.4

3.2.3

3.2.2

3.2.1

3.2.0

3.1.9

3.1.8

3.1.7

3.1.6

3.1.5

3.1.4

3.1.3

3.1.2

3.1.1

3.1.0

3.0.10

3.0.9

3.0.8

3.0.7

3.0.6

3.0.5

3.0.4

3.0.3

3.0.2

3.0.1

3.0.0

2.4.104

2.4.103

2.4.102

2.4.101

2.4.100

2.4.99

2.4.98

2.4.97

2.4.96

2.4.95

2.4.94

2.4.93

2.4.92

2.4.91

2.4.90

2.4.89

2.4.88

2.4.87

2.4.86

2.4.85

2.4.84

2.4.83

2.4.82

2.4.81

2.4.80

2.4.79

2.4.78

2.4.77

2.4.76

2.4.75

2.4.74

2.4.73

2.4.72

2.4.71

2.4.70

2.4.69

2.4.68

2.4.67

2.4.66

2.4.65

2.4.64

2.4.63

2.4.60

2.4.59

2.4.58

2.4.57

2.4.56

2.4.55

2.4.54

2.4.53

2.4.52

2.4.51

2.4.50

This version

2.4.49

2.4.48

2.4.47

2.4.45

2.4.44

2.4.43

2.4.42

2.4.41

2.4.40

2.4.39

2.4.38

2.4.37

2.4.36

2.4.35

2.4.34

2.4.33

2.4.32

2.4.31

2.4.29

2.4.28

2.4.25

2.4.24

2.4.23

2.4.22

2.4.21

2.4.20

2.4.19

2.4.18

2.4.17

2.4.16

2.4.15

2.4.14

2.4.13

2.4.12

2.4.11

2.4.10

2.4.9

2.4.8

2.4.7

2.4.6

2.4.5

2.4.4

2.4.3

2.4.2

2.4.1

2.4.0

2.3.2

2.3.1

2.3.0

2.2.28

2.2.27

2.2.26

2.2.25

2.2.24

2.2.23

2.2.21

2.2.20

2.2.19

2.2.18

2.2.17

2.2.16

2.2.15

2.2.14

2.2.13

2.2.12

2.2.11

2.2.10

2.2.9

2.2.8

2.2.7

2.2.6

2.2.5

2.2.4

2.2.3

2.2.2

2.2.1

2.2.0

2.1.92

2.1.91

2.1.90

2.1.89

2.1.88

2.1.87

2.1.86

2.1.85

2.1.84

2.1.83

2.1.82

2.1.81

2.1.80

2.1.79

2.1.78

2.1.77

2.1.76

2.1.74

2.1.73

2.1.71

2.1.70

2.1.69

2.1.68

2.1.67

2.1.66

2.1.65

2.1.64

2.1.63

2.1.62

2.1.61

2.1.60

2.1.59

2.1.58

2.1.57

2.1.56

2.1.55

2.1.54

2.1.53

2.1.52

2.1.51

2.1.50

2.1.49

2.1.48

2.1.47

2.1.46

2.1.45

2.1.44

2.1.43

2.1.42

2.1.41

2.1.40

2.1.39

2.1.38

2.1.37

2.1.36

2.1.35

2.1.34

2.1.33

2.1.32

2.1.31

2.1.30

2.1.29

2.1.28

2.1.27

2.1.26

2.1.25

2.1.24

2.1.22

2.1.21

2.1.20

2.1.19

2.1.18

2.1.17

2.1.16

2.1.15

2.1.14

2.1.13

2.1.12

2.1.11

2.1.10

2.1.9

2.1.8

2.1.7

2.1.6

2.1.5

2.1.4

2.1.3

2.1.2

2.1.1

2.1.0

2.0.10

2.0.9

2.0.8

2.0.7

2.0.6

2.0.5

2.0.4

2.0.3

2.0.2

2.0.1

1.0.10

1.0.9

1.0.8

1.0.7

1.0.6

1.0.5

1.0.4

1.0.3

1.0.2

1.0.1

Download files

Download the file for your platform. If you're not sure which to choose, learn more about installing packages.

Source Distribution

sure_tools-2.4.49.tar.gz (77.6 kB view details)

Uploaded Source

Built Distribution

If you're not sure about the file name format, learn more about wheel file names.

sure_tools-2.4.49-py3-none-any.whl (107.4 kB view details)

Uploaded Python 3

File details

Details for the file sure_tools-2.4.49.tar.gz.

File metadata

  • Download URL: sure_tools-2.4.49.tar.gz
  • Upload date:
  • Size: 77.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.10.18

File hashes

Hashes for sure_tools-2.4.49.tar.gz
Algorithm Hash digest
SHA256 569321c93a1367c05d17fa2693789f7d22bfe2602e9ab02cf4aa8f8a4cf9a4b9
MD5 4f249dfb7048a55d67be8ea7d271a319
BLAKE2b-256 1ec0467fbfdddb91386da83221124a9dae48d05b7613de8bf68a9ec9c6db6f95

See more details on using hashes here.

File details

Details for the file sure_tools-2.4.49-py3-none-any.whl.

File metadata

  • Download URL: sure_tools-2.4.49-py3-none-any.whl
  • Upload date:
  • Size: 107.4 kB
  • Tags: Python 3
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.10.18

File hashes

Hashes for sure_tools-2.4.49-py3-none-any.whl
Algorithm Hash digest
SHA256 a566642eca59257c5171df167ae4a633b5bb40fc55a5c4ce1d85e437df20e3da
MD5 ad94b00810213c46e7c40e7906ee3326
BLAKE2b-256 21db074d24111672167f00a41eb1d09e904b29e22393e7747f5eceb3da29a669

See more details on using hashes here.

Supported by

AWS Cloud computing and Security Sponsor Datadog Monitoring Depot Continuous Integration Fastly CDN Google Download Analytics Pingdom Monitoring Sentry Error logging StatusPage Status page