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samap

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

https://github.com/atarashansky/samap

Science Score: 46.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ○
    CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
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    .zenodo.json file
    Found .zenodo.json file
  • ○
    DOI references
  • ✓
    Academic publication links
    Links to: ncbi.nlm.nih.gov
  • ✓
    Committers with academic emails
    2 of 13 committers (15.4%) from academic institutions
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (12.5%) to scientific vocabulary

Keywords from Contributors

bioinformatics scverse anndata scanpy transcriptomics visualize-data
Last synced: 7 months ago · JSON representation

Repository

SAMap: Mapping single-cell RNA sequencing datasets from evolutionarily distant organisms.

Basic Info
  • Host: GitHub
  • Owner: atarashansky
  • License: mit
  • Language: Jupyter Notebook
  • Default Branch: main
  • Size: 150 MB
Statistics
  • Stars: 79
  • Watchers: 9
  • Forks: 20
  • Open Issues: 39
  • Releases: 0
Created over 5 years ago · Last pushed almost 2 years ago
Metadata Files
Readme License

README.md

SAMap -- version 1.0.15

Citation

Please cite the following paper if using SAMap: https://elifesciences.org/articles/66747

Tarashansky, Alexander J., et al. "Mapping single-cell atlases throughout Metazoa unravels cell type evolution." Elife 10 (2021): e66747.

Installation

pip

pip install samap

Manual installation

Download Anacodna from here: https://www.anaconda.com/download/

Create and activate a new environment for SAMap as follows:

```bash

Install SAMap dependencies availabe in conda

conda create -n SAMap -c conda-forge python=3.9 numpy=1.23.5 pip pybind11 h5py=3.8.0 leidenalg python-igraph texttable conda activate SAMap ```

Having activated the environment, install SAMap like so:

bash git clone https://github.com/atarashansky/SAMap.git samap_directory cd samap_directory pip install .

NCBI BLAST must be installed for the commandline.

```bash

Define NCBI BLAST version.

ncbiblastversion='2.9.0'

Download NCBI BLAST tarball.

wget "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${ncbiblastversion}/ncbi-blast-${ncbiblastversion}+-x64-linux.tar.gz"

Extract NCBI BLAST binaries in current conda environment bin directory.

tar -xzvf "ncbi-blast-${ncbiblastversion}+-x64-linux.tar.gz" \ -C "${CONDAPREFIX}/bin/" \ --strip-components=2 \ "ncbi-blast-${ncbiblast_version}+/bin/" ```

Alternatively, add the NCBI BLAST binaries manually to the path:

```bash

Define NCBI BLAST version.

ncbiblastversion='2.9.0'

Download NCBI BLAST tarball.

wget "ftp://ftp.ncbi.nlm.nih.gov/blast/executables/blast+/${ncbiblastversion}/ncbi-blast-${ncbiblastversion}+-x64-linux.tar.gz"

Extract NCBI BLAST tarball.

tar -xzvf "ncbi-blast-${ncbiblastversion}+-x64-linux.tar.gz"

Add NCBI BLAST programs to PATH.

echo "export PATH=\"$PATH:/your/directory/ncbi-blast-${ncbiblastversion}+/bin\"" >> ~/.bashrc source ~/.bashrc ```

Installation time should take no more than 10 minutes.

Running BLAST

The BLAST mapping script can be run from the SAMap_vignette.ipynb Jupyter notebook.

Depending on the number of cores available on your machine and the size/type of the input fasta files, this step may take up to around 4 hours.

Running SAMap

To run SAMap, use the SAMAP function in samap/mapping.py. Please see its function documentation for a description of the inputs and outputs. Take a look at the provided Jupyter notebook to get started (SAMap_vignette.ipynb).

Owner

  • Login: atarashansky
  • Kind: user

GitHub Events

Total
  • Issues event: 11
  • Watch event: 16
  • Issue comment event: 25
  • Fork event: 4
Last Year
  • Issues event: 11
  • Watch event: 16
  • Issue comment event: 25
  • Fork event: 4

Committers

Last synced: 12 months ago

All Time
  • Total Commits: 266
  • Total Committers: 13
  • Avg Commits per committer: 20.462
  • Development Distribution Score (DDS): 0.451
Past Year
  • Commits: 1
  • Committers: 1
  • Avg Commits per committer: 1.0
  • Development Distribution Score (DDS): 0.0
Top Committers
Name Email Commits
atarashansky t****n@s****u 146
atarashansky a****y@c****g 43
atarashansky a****y@C****t 23
atarashansky a****y@g****m 15
atarashansky a****y@c****m 12
atarashansky a****y@a****l 11
atarashansky a****y@C****l 9
Jonathan Manning j****g@e****k 2
chewc 3****c 1
Yishen Miao m****x@g****m 1
Tao Zhou 4****h 1
SeppeDeWinter s****r@h****m 1
Gert Hulselmans g****s@k****e 1
Committer Domains (Top 20 + Academic)
kuleuven.be: 1 ebi.ac.uk: 1 chanzuckerberg.com: 1 czimacos3990.hsd1.ma.comcast.net: 1 czbiohub.org: 1 stanford.edu: 1

Issues and Pull Requests

Last synced: 7 months ago

All Time
  • Total issues: 124
  • Total pull requests: 23
  • Average time to close issues: about 1 month
  • Average time to close pull requests: 4 days
  • Total issue authors: 76
  • Total pull request authors: 5
  • Average comments per issue: 3.16
  • Average comments per pull request: 0.04
  • Merged pull requests: 20
  • Bot issues: 0
  • Bot pull requests: 0
Past Year
  • Issues: 11
  • Pull requests: 0
  • Average time to close issues: 15 days
  • Average time to close pull requests: N/A
  • Issue authors: 11
  • Pull request authors: 0
  • Average comments per issue: 0.27
  • Average comments per pull request: 0
  • Merged pull requests: 0
  • Bot issues: 0
  • Bot pull requests: 0
View more stats
Top Authors
Issue Authors
  • atarashansky (11)
  • dariotommasini (5)
  • dkeitley (4)
  • houruiyan (4)
  • philoel (4)
  • wubaosheng (4)
  • JoshuaNguyen123 (3)
  • Smilenone (2)
  • otoky (2)
  • billadelonge (2)
  • kmmika (2)
  • ivanferrreira (2)
  • silastittes (2)
  • dsb66 (2)
  • PeiwenJi (2)
Pull Request Authors
  • atarashansky (21)
  • zEpoch (2)
  • pinin4fjords (1)
  • chewc (1)
  • mys721tx (1)
Top Labels
Issue Labels
Pull Request Labels

Packages

  • Total packages: 1
  • Total downloads:
    • pypi 104 last-month
  • Total dependent packages: 1
  • Total dependent repositories: 1
  • Total versions: 32
  • Total maintainers: 1
pypi.org: samap

The SAMap algorithm

  • Versions: 32
  • Dependent Packages: 1
  • Dependent Repositories: 1
  • Downloads: 104 Last month
Rankings
Dependent packages count: 4.8%
Forks count: 8.7%
Stargazers count: 9.5%
Average: 13.3%
Dependent repos count: 21.6%
Downloads: 21.8%
Maintainers (1)
tarashan
Last synced: 7 months ago

Dependencies

setup.py pypi
  • dill *
  • fast-histogram *
  • h5py ==3.8.0
  • hnswlib ==0.7.0
  • holoviews-samap *
  • leidenalg *
  • numba ==0.56.3
  • numpy ==1.23.5
  • sam-algorithm ==1.0.2
  • scanpy ==1.9.3