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data_challenges_tools.Rmd
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---
title: "Data Challenges 2019: TOOLS"
output:
html_document:
includes:
in_header: cover.html
---
Some tools that you can use (non-exhaustive)
### Methylome
#### Unsupervised
[RefFreeEWAS](https://cran.r-project.org/web/packages/RefFreeEWAS/index.html)
Houseman et al, 2016, BMC bioinformatics, PMID 27358049 **[NMF]**
[MeDeCom](https://github.com/lutsik/MeDeCom)
Lutsik et al, 2017, Genome Biology, PMID 28340624 **[NMF]**
#### Semi-supervised
[EDec](https://github.com/BRL-BCM/EDec)
Onuchic et al, 2017, Cell reports, PMID 27851969 **[NMF]**
#### Supervised
[EpiDISH](https://github.com/sjczheng/EpiDISH)
Teschendorff et al, 2017, Epigenomics, PMID 28517979 **[SVR, RPC or CP]**
##### Toolbox R package
[medepir](https://bcm-uga.github.io/medepir/index.html)
Decamps et al, 2019, In revision in BMC Bioinformatics, **[pipeline for RefFree methods]**
##### *Reference*
[https://github.com/lutsik/CellTypeInferenceMethods](https://github.com/lutsik/CellTypeInferenceMethods)
### Transcriptome
#### Unsupervised
[DeconICA](https://urszulaczerwinska.github.io/DeconICA/)
Czerwinska et al. **[ICA]**
[Decoder](https://github.com/laurapeng/decoder)
Peng et al 2019, Nature communications. **[NMF + NNLS]**
[deconf](https://bmcbioinformatics.biomedcentral.com/articles/10.1186/1471-2105-11-27)
Repsilber et al., 2010, BMC bioinformatics. **[Random Forest + NNLS]**
#### Semi-supervised
[Deblender](https://github.com/kondim1983/Deblender/)
Dimitrakopoulou et al 2018, Bioinformatics. **[NMF]**(MATLAB)
[WISP](https://cit-bioinfo.github.io/WISP/)
Blum et al 2019, Nature communications. **[NNLS]**
[DSA](https://github.com/zhandong/DSA)
Zhong et al., 2013, BMC bioinformatics. **[NNLS]**
#### Supervised
[DeconvSeq](https://github.com/rosedu1/deconvSeq)
Du et al 2019 Bioinformatics. **[GLM]**
[LRCDE](https://github.com/ERGlass/lrcde.dev)
Glass and Dozmorov, 2016, BMC bioinformatics. **[LM]**
[MMAD](http://sourceforge.net/projects/mmad/)
Liebner et al 2014, Bioinformatics. **[Maximum likelihood/ Conjugate gradient]**(MATLAB)
[DeconRNASeq](https://www.bioconductor.org/packages/release/bioc/html/DeconRNASeq.html)
Gong and Szustakowski, 2013, Bioinformatics. **[NNLS]**
[MuSic](https://github.com/xuranw/MuSiC)
Wang et al 2019, Nature communications. **[NNLS]**
##### Toolbox R package
[CellMix](web.cbio.uct.ac.za/~renaud/CRAN/web/CellMix)
Gaujoux and Seoighe, 2013, Bioinformatics. **[including DSA and deconf, NMF]**
##### *Reference*
[Avila Cobos, F., Vandesompele, J., Mestdagh, P., & De Preter, K. (2018). Computational deconvolution of transcriptomics data from mixed cell populations. Bioinformatics, 34(11), 1969-1979.](https://academic.oup.com/bioinformatics/article/34/11/1969/4813737)