Ecosyste.ms: Papers

An open API service providing mapping between scientific papers and software projects that are mentioned in them.
All mentions data is based on the CZI Software Mentions dataset.

Papers: 10.1186/s13059-021-02295-1

https://doi.org/10.1186/s13059-021-02295-1

gapseq: informed prediction of bacterial metabolic pathways and reconstruction of accurate metabolic models

Cited by: 77
Author(s): Johannes Zimmermann, Christoph Kaleta, Silvio Waschina
Published: over 3 years ago

Software Mentions 18

cran: BacArena
Modeling Framework for Cellular Communities in their Environments
Papers that mentioned: 19
cran: doParallel
Foreach Parallel Adaptor for the 'parallel' Package
Papers that mentioned: 90
cran: factoextra
Extract and Visualize the Results of Multivariate Data Analyses
Papers that mentioned: 650
cran: foreach
Provides Foreach Looping Construct
Papers that mentioned: 50
cran: getopt
C-Like 'getopt' Behavior
Papers that mentioned: 3
cran: glpkAPI
R Interface to C API of GLPK
Papers that mentioned: 4
cran: merlin
Mixed Effects Regression for Linear, Non-Linear and User-Defined Models
Papers that mentioned: 18
cran: reshape2
Flexibly Reshape Data: A Reboot of the Reshape Package
Papers that mentioned: 421
cran: R.utils
Various Programming Utilities
Papers that mentioned: 13
cran: stringi
Fast and Portable Character String Processing Facilities
Papers that mentioned: 34
cran: stringr
Simple, Consistent Wrappers for Common String Operations
Papers that mentioned: 172
cran: sybil
Efficient Constrained Based Modelling
Papers that mentioned: 12
pypi: carveme
CarveMe: automated metabolic model reconstruction
Papers that mentioned: 1
pypi: data
Work with unicode/non-unicode data from files or strings uniformly.
Papers that mentioned: 33
pypi: merlin
The building blocks of workflows!
Papers that mentioned: 18
pypi: PythonCyc
A Python interface to Pathway Tools, 2019 update
Papers that mentioned: 1
pypi: sh
Python subprocess replacement
Papers that mentioned: 48
pypi: sybil
Automated testing for the examples in your code and documentation.
Papers that mentioned: 12