:: DESCRIPTION
RefineTree is a gene tree correction software, based on resolving a multifurcated gene tree in a way minimizing the reconciliation distance with a given species tree.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
NO
:: MORE INFORMATION
Citation
Genome evolution-aware gene trees
E. Noutahi, M. Semeria, M. Lafond, J. Seguin, B. Boussau, L. Gueguen, N. El-Mabrouk and Eric Taniier,
submitted to PloS.Comp.Biol, 2015.
:: DESCRIPTION
RNASeqBias contains functions and sample data for detecting and correcting for biases in gene expression levels from RNA-Seq experiments. Considered bias factors are gene length, GC content and dinucleotide frequencies. Principal component analysis on GC content and dinucleotide frequencies are first performed, and the resulting principal components and gene length were used as covariates to fit a generalized additive model with smoothing spline on gene expression levels as response. The package also have codes to generate bias plots before and after bias correction, and to compare with other quantitative platforms.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
BMC Bioinformatics. 2011 Jul 19;12:290. doi: 10.1186/1471-2105-12-290.
Bias detection and correction in RNA-Sequencing data.
Zheng W1, Chung LM, Zhao H.
:: DESCRIPTION
CopyNumber450kCancer takes the output of CopyNumber450k and ChAMP packages and correct the baseline in each sample for accurate copy number calling, specially in cancer samples. CopyNumber450kCancer can read the segment output file from CopyNumber450k package directly without any need for modification. Output files from ChAMP need to be in one file not in seperated files.
::DEVELOPER
Molecular Medicine research group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
CopyNumber450kCancer: Baseline Correction for Accurate Copy Number Calling from the 450k Methylation Array.
Marzouka NA, Nordlund J, Bäcklin CL, Lönnerholm G, Syvänen AC, Almlöf JC.
Bioinformatics. 2015 Nov 9. pii: btv652
:: DESCRIPTION
LMM-Lasso is a linear mixed models that allows for both multi-locus mapping and correction for confounding effects.
::DEVELOPER
Machine Learning and Computational Biology Research Group
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Jan 15;29(2):206-14. doi: 10.1093/bioinformatics/bts669.
A Lasso multi-marker mixed model for association mapping with population structure correction.
Rakitsch B, Lippert C, Stegle O, Borgwardt K.
:: DESCRIPTION
NIACS implements a method for deffining causal networks corrected for the problem of interference between dynamically similar regulators within the context of a sparse linear auto-regression model.
::DEVELOPER
The Warwick Systems Biology Centre (WSB)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Correcting for link loss in causal network inference caused by regulator interference.
Wang Y, Penfold CA, Hodgson DA, Gifford ML, Burroughs NJ.
Bioinformatics. 2014 Jun 19. pii: btu388.
:: DESCRIPTION
ACE corrects substitution errors in an Illumina archive using a k-mer trie.
::DEVELOPER
:: SCREENSHOTS
N/a
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
ACE: Accurate Correction of Errors using K-mer tries.
Sheikhizadeh S, de Ridder D.
Bioinformatics. 2015 May 28. pii: btv332.
:: DESCRIPTION
CorQ (Correction through Quality) is a new algorithm which utilizes the inherent base quality in a sequence-specific context to correct for homopolymer and non-homopolymer insertion and deletion (indel) errors.
::DEVELOPER
Mullins Molecular Retrovirology Lab, University of Washington.
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
PLoS One. 2013 Sep 5;8(9):e73015. doi: 10.1371/journal.pone.0073015. eCollection 2013.
Quality score based identification and correction of pyrosequencing errors.
Iyer S1, Bouzek H, Deng W, Larsen B, Casey E, Mullins JI.
:: DESCRIPTION
RACER is a C++/OpenMP program that corrects sequencing errors in high-throughput DNA sequencing data, especially designed for the Illumina platform.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
Bioinformatics. 2013 Oct 1;29(19):2490-3. doi: 10.1093/bioinformatics/btt407. Epub 2013 Jul 12.
RACER: Rapid and accurate correction of errors in reads.
Ilie L1, Molnar M.
:: DESCRIPTION
HiTEC (High Throughput Error Correction) , an algorithm that provides a highly accurate, robust and fully automated method to correct reads produced by high-throughput sequencing methods. The approach provides significantly higher accuracy than previous methods. It is time and space efficient and works very well for all read lengths, genome sizes and coverage levels.
::DEVELOPER
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation
L. Ilie, F. Fazayeli, S. Ilie,
HiTEC: accurate error correction in high-throughput sequencing data,
Bioinformatics 27(3) (2011) 295 — 302.
:: DESCRIPTION
LoRDEC is a program to correct sequencing errors in long reads from 3rd generation sequencing with high error rate, and is especially intended for PacBio reads.
::DEVELOPER
The Computational Biology Institute (IBC)
:: SCREENSHOTS
N/A
:: REQUIREMENTS
:: DOWNLOAD
:: MORE INFORMATION
Citation:
Bioinformatics. 2014 Aug 26. pii: btu538.
LoRDEC: accurate and efficient long read error correction.
Salmela L, Rivals E.
