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

This version

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-2.4.39.tar.gz (85.6 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-2.4.39-py3-none-any.whl (107.0 kB view details)

Uploaded Python 3

File details

Details for the file sure_tools-2.4.39.tar.gz.

File metadata

  • Download URL: sure_tools-2.4.39.tar.gz
  • Upload date:
  • Size: 85.6 kB
  • Tags: Source
  • Uploaded using Trusted Publishing? No
  • Uploaded via: twine/6.2.0 CPython/3.10.18

File hashes

Hashes for sure_tools-2.4.39.tar.gz
Algorithm Hash digest
SHA256 2f585651d6df359391751b73d9b8fd561be6d3d6d5cde6f91512c58f65912cac
MD5 7b6c98fac5ed6617d91665b24990035c
BLAKE2b-256 75b1eae953fa0814a6eec36bf579c602d6e4f915bb4e5fce051486d4a06e2315

See more details on using hashes here.

File details

Details for the file sure_tools-2.4.39-py3-none-any.whl.

File metadata

  • Download URL: sure_tools-2.4.39-py3-none-any.whl
  • Upload date:
  • Size: 107.0 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-2.4.39-py3-none-any.whl
Algorithm Hash digest
SHA256 6964f350830f58524ab55227d90dc501a67c8fc9543f91c237804be001ad8368
MD5 8b0e4b3f69438b7da94be7a4eecd1270
BLAKE2b-256 47eabce96438afe57ac68d4d8474dea2f49468bb52f28c2a06b529e129e05f06

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