clonealign 2.0 – Bayesian Inference of clone-specific Gene Expression Estimates

clonealign 2.0

:: DESCRIPTION

clonealign assigns single-cell RNA-seq expression to cancer clones by probabilistically mapping RNA-seq to clone-specific copy number profiles using reparametrization gradient variational inference.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux / MacOsX / Windows
R

:: DOWNLOAD

clonealign

:: MORE INFORMATION

Citation

Genome Biol. 2019 Mar 12;20(1):54. doi: 10.1186/s13059-019-1645-z.
clonealign: statistical integration of independent single-cell RNA and DNA sequencing data from human cancers.
Campbell KR, etc.

PseudoLasso v2 – Efficient approach to correct Read Alignment for Pseudogene Abundance Estimates

PseudoLasso v2

:: DESCRIPTION

PseudoLasso is a linear regression approach to learn read alignment behaviors, and to leverage this knowledge for abundance estimation and alignment correction.

::DEVELOPER

Wei Wang

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Windows/Linux/MacOsX
Python

:: DOWNLOAD

PseudoLasso

:: MORE INFORMATION

Citation

Ju CJ, Zhao Z, Wang W.
Efficient Approach to Correct Read Alignment for Pseudogene Abundance Estimates.
IEEE/ACM Trans Comput Biol Bioinform. 2017 May-Jun;14(3):522-533. doi: 10.1109/TCBB.2016.2591533. Epub 2016 Jul 14. PMID: 27429446; PMCID: PMC5514313.

Parat 0.9.1 – Estimates Site Specific Substitution Rates from a set of DNA sequences

Parat 0.9.1

:: DESCRIPTION

parat estimates site specific substitution rates from a set of DNA sequences. The rates and the phylogenetic tree relating the sequences are estimated in an iterative maximum likelihood procedure, whereby the likelihood of the inferred tree increases at each iteration step until it converges.

::DEVELOPER

the Center of Integrative Bioinformatics Vienna (CIBIV) headed by Arndt von Haeseler.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

Linux

:: DOWNLOAD

parat

:: MORE INFORMATION

Citation:

S. Meyer and A. von Haeseler (2003)
Identifying site specific substitution rates.
Mol. Biol. Evol., 20, 182-189.