SigProfilerExtractor VS scispacy

Compare SigProfilerExtractor vs scispacy and see what are their differences.

SigProfilerExtractor

SigProfilerExtractor allows de novo extraction of mutational signatures from data generated in a matrix format. The tool identifies the number of operative mutational signatures, their activities in each sample, and the probability for each signature to cause a specific mutation type in a cancer sample. The tool makes use of SigProfilerMatrixGenerator and SigProfilerPlotting. (by AlexandrovLab)
Bioinformatics somatic-variants cancer-genomics mutational-signatures mutation-analysis
Source Code
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scispacy

A full spaCy pipeline and models for scientific/biomedical documents. (by allenai)
scientific-documents spacy custom-pipes NLP biomedical Bioinformatics
Source Code
allenai.github.io
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SigProfilerExtractor scispacy
1 2
146 1,616
2.7% 1.4%
3.5 6.7
16 days ago about 1 month ago
Python Python
BSD 2-clause "Simplified" License Apache License 2.0
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SigProfilerExtractor

Posts with mentions or reviews of SigProfilerExtractor. We have used some of these posts to build our list of alternatives and similar projects.

scispacy

Posts with mentions or reviews of scispacy. We have used some of these posts to build our list of alternatives and similar projects. The last one was on 2022-11-05.
  • Guidance needed: Extracting diseases and symptoms from medical text
    2 projects | /r/LanguageTechnology | 5 Nov 2022
    https://github.com/medspacy/medspacy and https://allenai.github.io/scispacy/ should get you most of the way there
  • Installing SciSpacy on Apple M1 Laptops
    1 project | dev.to | 10 Jul 2022
    The ** pip install -r requirement.txt ** failed with lot of errors while installing a dependency ** nmslib ** with an error ** clang compiler does not support '-march=native' **. Since I already had the Xcode installed on my Mac the version of C was 11 but somehow the mentioned command was failing, since the said argument was not supported on the C version. With a lot of digging around I finally found a solution mentioned on SciSpacy GitHub page.

What are some alternatives?

When comparing SigProfilerExtractor and scispacy you can also consider the following projects:

sv-callers - Snakemake-based workflow for detecting structural variants in genomic data

medspacy - Library for clinical NLP with spaCy.

deepvariant - DeepVariant is an analysis pipeline that uses a deep neural network to call genetic variants from next-generation DNA sequencing data.

rasa - 💬 Open source machine learning framework to automate text- and voice-based conversations: NLU, dialogue management, connect to Slack, Facebook, and more - Create chatbots and voice assistants

Biopython - Official git repository for Biopython (originally converted from CVS)

spaCy - 💫 Industrial-strength Natural Language Processing (NLP) in Python

scanpy - Single-cell analysis in Python. Scales to >1M cells.

spacy-models - 💫 Models for the spaCy Natural Language Processing (NLP) library

typedb-bio - TypeDB Bio: Biomedical Knowledge Graph

SigProfilerExtractor vs sv-callers scispacy vs medspacy SigProfilerExtractor vs deepvariant scispacy vs rasa SigProfilerExtractor vs Biopython scispacy vs spaCy SigProfilerExtractor vs scanpy scispacy vs spacy-models scispacy vs typedb-bio