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

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

This version

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-2.4.22.tar.gz (76.7 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-2.4.22-py3-none-any.whl (88.6 kB view details)

Uploaded Python 3

File details

Details for the file sure_tools-2.4.22.tar.gz.

File metadata

  • Download URL: sure_tools-2.4.22.tar.gz
  • Upload date:
  • Size: 76.7 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.10.18

File hashes

Hashes for sure_tools-2.4.22.tar.gz
Algorithm Hash digest
SHA256 509bbb78184d15d8e061d2b22ae18e7e80754622a7549243e35beb149133c698
MD5 e27526920fe90ef8d6c4d81aa18c1568
BLAKE2b-256 9d7f880354311080f784f3905d709501761f420782b867c4454d21751e4405c8

See more details on using hashes here.

File details

Details for the file sure_tools-2.4.22-py3-none-any.whl.

File metadata

  • Download URL: sure_tools-2.4.22-py3-none-any.whl
  • Upload date:
  • Size: 88.6 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-2.4.22-py3-none-any.whl
Algorithm Hash digest
SHA256 933115e05f4009f62e48cb9ae6e9c5fffd2319798fe043a80fa8d91b67ebbbee
MD5 26dd0bcc5fdc77f00a94823052357e11
BLAKE2b-256 d1eb928eabd39c111f19da908ade38dd3c9ddca8dbe9d39b2f5d8d6598d11eb3

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