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

This version

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

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-2.4.51.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-2.4.51-py3-none-any.whl (107.4 kB view details)

Uploaded Python 3

File details

Details for the file sure_tools-2.4.51.tar.gz.

File metadata

  • Download URL: sure_tools-2.4.51.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-2.4.51.tar.gz
Algorithm Hash digest
SHA256 e4f6e7112d24aee27fd9d97e38ad5f87cd634530020afff3c4284dc5f92e46b8
MD5 3383df60d6a58159f557d8e2bf8ab692
BLAKE2b-256 b3441249284e6f3b4f88a2fbb3cc0a718d2bd2f8d663aee02b57016668b8b0e6

See more details on using hashes here.

File details

Details for the file sure_tools-2.4.51-py3-none-any.whl.

File metadata

  • Download URL: sure_tools-2.4.51-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-2.4.51-py3-none-any.whl
Algorithm Hash digest
SHA256 aead5b8143e7b9697d35cbe3ff5c79ec7681905e83f5646cb415929ebab5a2b8
MD5 a0ce2a5fa100c44d4f5786012ea51449
BLAKE2b-256 2b17fd0dce01ee9a3e33c9ca0fae8ed749b04eb83a7f90e88a3d4f8d2d826d5f

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