README.md
In bioarch-sjh/bacollite: Analysis of MALDI and LC-MS/MS spectral data using sequence data (mainly for collagen)
The bacollite package offers a set of tools for aligning MALDI spectrum data with 'theroretical' peak positions that have been calculated from sequence and chemistry data. The alignment is carried out by cross-corelation and yields a correlation score and a lag score, both of which can be used to determine the presence or absence of a peptide in the spectrum.
Installation
see INSTALL.md in this directory
User guides
bacollite is under active development. Please contact us or raise an issue if you need help!
A vignette called "Aligning Samples To Peptides for Sheep, Cow, Goat and Deer" is available that will guide you through the process of loading data, aligning peptides and performing classifications. This can be found by typing browseVignettes("bacollite") at the R console. More vignettes will be added soon.
References
This software is free, but if you use it in an academic paper, please cite the following:
Simon Hickinbotham, Sarah Fiddyment, Timothy L Stinson, Matthew J Collins (2020)
How to Get Your Goat: Automated Identification of Species from MALDI-ToF Spectra
Bioinformatics, March 2020
DOI 10.1093/bioinformatics/btaa181
Pubmed ID 32176274
https://t.co/13DKasOLQe
The analysis in the above paper was carried out using version 1.0.0 of this software
Publications using bacollite
Richter, Kristine Korzow and McGrath, Krista and Masson-MacLean, Edouard and Hickinbotham, Simon and Tedder, Andrew and Britton, Kate and Bottomley, Zoe and Dobney, Keith and Hulme-Beaman, Ardern and Zona, Margherita et al (2020) What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon Journal of Archaeological Science 116:105116, 2020.
The analysis in the above paper was carried out using version 0.0.2 of this software
bioarch-sjh/bacollite documentation built on Oct. 7, 2022, 3:34 p.m.
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
The bacollite package offers a set of tools for aligning MALDI spectrum data with 'theroretical' peak positions that have been calculated from sequence and chemistry data. The alignment is carried out by cross-corelation and yields a correlation score and a lag score, both of which can be used to determine the presence or absence of a peptide in the spectrum.
Installation
see INSTALL.md in this directory
User guides
bacollite is under active development. Please contact us or raise an issue if you need help!
A vignette called "Aligning Samples To Peptides for Sheep, Cow, Goat and Deer" is available that will guide you through the process of loading data, aligning peptides and performing classifications. This can be found by typing browseVignettes("bacollite") at the R console. More vignettes will be added soon.
References
This software is free, but if you use it in an academic paper, please cite the following:
Simon Hickinbotham, Sarah Fiddyment, Timothy L Stinson, Matthew J Collins (2020) How to Get Your Goat: Automated Identification of Species from MALDI-ToF Spectra Bioinformatics, March 2020 DOI 10.1093/bioinformatics/btaa181 Pubmed ID 32176274 https://t.co/13DKasOLQe
The analysis in the above paper was carried out using version 1.0.0 of this software
Publications using bacollite
Richter, Kristine Korzow and McGrath, Krista and Masson-MacLean, Edouard and Hickinbotham, Simon and Tedder, Andrew and Britton, Kate and Bottomley, Zoe and Dobney, Keith and Hulme-Beaman, Ardern and Zona, Margherita et al (2020) What's the catch? Archaeological application of rapid collagen-based species identification for Pacific Salmon Journal of Archaeological Science 116:105116, 2020.
The analysis in the above paper was carried out using version 0.0.2 of this software
R Package Documentation
Browse R Packages
We want your feedback!
Note that we can't provide technical support on individual packages. You should contact the package authors for that.
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