:: DESCRIPTION
FacPad is an R package implementing a Bayesian sparse factor model for the inference of pathways responsive to drug treatment.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Oct 15;28(20):2662-70. doi: 10.1093/bioinformatics/bts502. Epub 2012 Aug 24.
FacPad: Bayesian sparse factor modeling for the inference of pathways responsive to drug treatment.
Ma H, Zhao H.
:: DESCRIPTION
Inferelator learns parsimonious regulatory networks from systems biology datasets.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Alex Greenfield, Christoph Hafemeister, and Richard Bonneau
Robust data-driven incorporation of prior knowledge into the inference of dynamic regulatory networks
Bioinformatics (2013) 29 (8): 1060-1067. doi:10.1093/bioinformatics/btt099
:: DESCRIPTION
iFad is an R package implementing a bayesian sparse factor model for the joint analysis of paired datasets, the gene expression and drug sensitivity profiles, measured across the same panel of samples, e.g. cell lines.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2012 Jul 15;28(14):1911-8. doi: 10.1093/bioinformatics/bts285. Epub 2012 May 10.
iFad: an integrative factor analysis model for drug-pathway association inference.
Ma H, Zhao H.
:: DESCRIPTION
HaploPOP is a software to build informative haplotypes for population genetic structure inference.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Duforet-Frebourg N., Gattepaille L.M., Blum M.G.B and Jakobsson M.
Haplopop: a software that improves population assignment by combining markers into haplotypes.
(in prep)
:: DESCRIPTION
ClonalFrame is a computer package for the inference of bacterial microevolution using multilocus sequence data.In a nutshell, ClonalFrame identifies the clonal relationships between the members of a sample, while also estimating the chromosomal position of homologous recombination events that have disrupted the clonal inheritance.ClonalFrame can be applied to any kind of sequence data, from a single fragment of DNA to whole genomes. It is well suited for the analysis of MLST data, where 7 gene fragments have been sequenced, but becomes progressively more powerful as the sequenced regions increase in length and number up to whole genomes. However, it requires the sequences to be aligned. If you have genomic data that is not aligned, we recommend using Mauve which produces alignment of whole bacterial genomes in exactly the format required for analysis with ClonalFrame.
ClonalFrameML is a software package that performs efficient inference of recombination in bacterial genomes.
::DEVELOPER
Xavier Didelot and Daniel Wilson
:: SCREENSHOTS
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ClonalFrameML: efficient inference of recombination in whole bacterial genomes.
Didelot X, Wilson DJ.
PLoS Comput Biol. 2015 Feb 12;11(2):e1004041. doi: 10.1371/journal.pcbi.1004041.
Didelot and Falush (2007)
Inference of Bacterial Microevolution Using Multilocus Sequence Data
Genetics March 2007 vol. 175 no. 3 1251-1266
:: DESCRIPTION
PIA is a toolbox for MS based protein inference and identification analysis.
::DEVELOPER
Medizinisches Proteom-Center, Medical Bioinformatics
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PIA: An Intuitive Protein Inference Engine with a Web-Based User Interface.
Uszkoreit J, Maerkens A, Perez-Riverol Y, Meyer HE, Marcus K, Stephan C, Kohlbacher O, Eisenacher M.
J Proteome Res. 2015 Jul 2;14(7):2988-97. doi: 10.1021/acs.jproteome.5b00121
:: DESCRIPTION
Infernal (INFERence of RNA ALignment) is for searching DNA sequence databases for RNA structure and sequence similarities. It is an implementation of a special case of profile stochastic context-free grammars called covariance models (CMs). A CM is like a sequence profile, but it scores a combination of sequence consensus and RNA secondary structure consensus, so in many cases, it is more capable of identifying RNA homologs that conserve their secondary structure more than their primary sequence.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
E. P. Nawrocki, D. L. Kolbe, and S. R. Eddy
Infernal 1.0: Inference of RNA alignments
Bioinformatics 25:1335-1337 (2009), .
:: DESCRIPTION
SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
pySCENIC is a lightning-fast python implementation of the SCENIC pipeline (Single-Cell rEgulatory Network Inference and Clustering) which enables biologists to infer transcription factors, gene regulatory networks and cell types from single-cell RNA-seq data.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Aibar S, et al.
SCENIC: single-cell regulatory network inference and clustering.
Nat Methods. 2017 Nov;14(11):1083-1086. doi: 10.1038/nmeth.4463. Epub 2017 Oct 9. PMID: 28991892; PMCID: PMC5937676.
Van de Sande B,et al.
A scalable SCENIC workflow for single-cell gene regulatory network analysis.
Nat Protoc. 2020 Jul;15(7):2247-2276. doi: 10.1038/s41596-020-0336-2. Epub 2020 Jun 19. PMID: 32561888.
:: DESCRIPTION
EFICAz2 (Enzyme Function Inference by a Combined Approach) is an automatic engine for large-scale enzyme function inference that combines predictions from six different methods developed and optimized to achieve high prediction accuracy: (i) recognition of functionally discriminating residues (FDRs) in enzyme families obtained by a Conservation-controlled HMM Iterative procedure for Enzyme Family classification (CHIEFc), (ii) pairwise sequence comparison using a family specific Sequence Identity Threshold, (iii) recognition of FDRs in Multiple Pfam enzyme families, (iv) recognition of multiple Prosite patterns of high specificity, (v) SVM evaluation of CHIEFc families, and (vi) SVM evaluation of Multiple Pfam enzyme families.
::DEVELOPER
Center for the Study of Systems Biology
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Arakaki A, Huang Y and Skolnick J (2009) EFICAz2: enzyme function inference by a combined approach enhanced by machine learning. BMC Bioinformatics 10:107
:: DESCRIPTION
INSIGHT is a method for inferring signatures of recent natural selection from patterns of polymorphism and divergence across a collection of short dispersed genomic elements.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Gronau I, Arbiza L, Mohammed J, Siepel A.
Inference of natural selection from interspersed genomic elements based on polymorphism and divergence.
Mol Biol Evol. 2013 May;30(5):1159-71. doi: 10.1093/molbev/mst019. Epub 2013 Feb 5. PMID: 23386628; PMCID: PMC3697874.
