BioIDMapper 3.0 – Mapping Biological IDs

BioIDMapper 3.0

:: DESCRIPTION

BioIDMapper is a Cross-referencing and Managing Platform for Biological IDs in R.

:: DEVELOPER

Dr. Xiaoyong Sun, Genomics and Bioinformatics Laboratory

:: SCREENSHOTS

BioIDMapper

:: REQUIREMENTS

  • Linux / WIndows
  • R

:: DOWNLOAD

 BioIDMapper

:: MORE INFORMATION

Citation

Xiaoyong Sun, Michael Lawrence, Zhaoquan Liu, Zhongxu Sun.
BioIDMapper: a Cross-referencing and Managing Platform for Biological IDs in R.
the 3rd International Conference on BioMedical Engineering and Informatics (BMEI 2010). Oct 16-18, 2010. Yantai, China.

HAPAL – Mapping HAPlotype-haplotype Interactions with Adaptive Lasso

HAPAL

:: DESCRIPTION

HAPAL is an R code for mapping HAPlotype-haplotype interactions with Adaptive Lasso

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 HAPAL

:: MORE INFORMATION

Citation:

BMC Genet. 2010 Aug 27;11:79. doi: 10.1186/1471-2156-11-79.
Mapping haplotype-haplotype interactions with adaptive LASSO.
Li M, Romero R, Fu WJ, Cui Y.

iQTL-VC – iQTL mapping with Variance Component mode

iQTL-VC

:: DESCRIPTION

iQTL-VC is an R code for iQTL mapping with Variance Component model in experimental cross.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • R

:: DOWNLOAD

 iQTL-VC

:: MORE INFORMATION

Citation:

Li, G.X. and Y.H. Cui. (2010)
A general statistical framework for dissecting parent-of-origin effects underlying triploid endosperm traits in flowering plants.
Annals of Applied Statistics 4(3): 1214-1233.

QTL-GPR – QTL Mapping with Count Trait

QTL-GPR

:: DESCRIPTION

QTL-GPR (quantitative trait loci – Generalized Poisson Regression) is a Matlab code for QTL mapping with count trait.

::DEVELOPER

Yuehua Cui, Ph.D.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • MatLab

:: DOWNLOAD

 QTL-GPR

:: MORE INFORMATION

Citation:

Genetics. 2006 Dec;174(4):2159-72. Epub 2006 Oct 8.
On the generalized poisson regression mixture model for mapping quantitative trait loci with count data.
Cui Y1, Kim DY, Zhu J.

MetaMapp – Mapping and Visualizing Metabolomic data

MetaMapp

:: DESCRIPTION

MetaMapp is a tool to construct metabolomics network graphs from the chemical similarity and mass spectral similarity matrices and the KEGG reaction pair database.

::DEVELOPER

The Fiehn laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2012 May 16;13:99.
MetaMapp: mapping and visualizing metabolomic data by integrating information from biochemical pathways and chemical and mass spectral similarity.
Barupal DK, Haldiya PK, Wohlgemuth G, Kind T, Kothari SL, Pinkerton KE, Fiehn O.

GPU-BSM 2.7.1 – BS-treated Reads Mapping Tool

GPU-BSM 2.7.1

:: DESCRIPTION

GPU-BSM (GPU-BiSulfite reads Mapping) is a GPU-based tool devised to map bisulfite-treated reads.

::DEVELOPER

the National Institute of Biomedical Technologies, The National Research Council (CNR) , Italy

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • CUDA (release ≥6.0).

:: DOWNLOAD

 GPU-BSM

:: MORE INFORMATION

Citation

PLoS One. 2014 May 19;9(5):e97277. doi: 10.1371/journal.pone.0097277. eCollection 2014.
GPU-BSM: a GPU-based tool to map bisulfite-treated reads.
Manconi A, Orro A, Manca E, Armano G, Milanesi L

GLOOME 201305 – Gain Loss Mapping Engine

GLOOME 201305

:: DESCRIPTION

The main purpose of GLOOME server is to accurately infers branch specific and site specific gain and loss events.

:: DEVELOPER

Edmond J. Safra Center for Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 GLOOME

:: MORE INFORMATION

Citation:

Genome Biol Evol. 2011;3:1265-75. doi: 10.1093/gbe/evr101. Epub 2011 Oct 4.
Inference of gain and loss events from phyletic patterns using stochastic mapping and maximum parsimony–a simulation study.
Cohen O1, Pupko T.

GLOOME: gain loss mapping engine.
Cohen O, Ashkenazy H, Belinky F, Huchon D, Pupko T.
Bioinformatics. 2010 Nov 15;26(22):2914-5. doi: 10.1093/bioinformatics/btq549.

SNPAAMapper 2.0 – A SNP Amino Acid Mapping tool

SNPAAMapper 2.0

:: DESCRIPTION

SNPAAMapper is a downstream variant annotation program that can effectively classify variants by region (e.g. exon, intron, etc), predict amino acid change type (e.g. synonymous, non-synonymous mutation, etc), and prioritize mutation effects (e.g. CDS versus 5’UTR, etc).

::DEVELOPER

Computational Biology Lab at Indiana State University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • PErl

:: DOWNLOAD

  SNPAAMapper

:: MORE INFORMATION

Citation

Bioinformation. 2013 Oct 16;9(17):870-2. doi: 10.6026/97320630009870. eCollection 2013.
SNPAAMapper: An efficient genome-wide SNP variant analysis pipeline for next-generation sequencing data.
Bai Y1, Cavalcoli J.

CoLoRMap – Correcting Long noisy Reads by Mapping short reads

CoLoRMap

:: DESCRIPTION

CoLoRMap is a hybrid method for correcting noisy long reads, such as the ones produced by PacBio sequencing technology, using high-quality Illumina paired-end reads mapped onto the long reads.

::DEVELOPER

Lab for Bioinformatics and Computational Genomics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

CoLoRMap 

:: MORE INFORMATION

Citation

Haghshenas E, Hach F, Sahinalp SC, Chauve C.
CoLoRMap: Correcting Long Reads by Mapping short reads.
Bioinformatics. 2016 Sep 1;32(17):i545-i551. doi: 10.1093/bioinformatics/btw463. PMID: 27587673.