ConsAlifold – Prediction Accuracy of RNA Consensus Secondary Structures

:: DESCRIPTION

Retired Neurosurgeon Have Fun at Work Tomorrow Retirement Gi Pul is a dynamic programming-based method that predicts the consensus secondary structure of an RNA sequence alignment.

::DEVELOPER

ConsAlifold team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

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:: MORE INFORMATION

Citation

Tagashira M, Asai K.
ConsAlifold: Considering RNA Structural Alignments Improves Prediction Accuracy of RNA Consensus Secondary Structures.
Bioinformatics. 2021 Oct 25:btab738. doi: 10.1093/bioinformatics/btab738. Epub ahead of print. PMID: 34694364.

MetaClean 1.0.0 – Detection of Low-Quality Peaks in Untargeted Metabolomics Data

:: DESCRIPTION

MetaClean is a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data

::DEVELOPER

Jan Krumsiek lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

MetaClean

:: MORE INFORMATION

Citation

Chetnik K, Petrick L, Pandey G.
MetaClean: a machine learning-based classifier for reduced false positive peak detection in untargeted LC-MS metabolomics data.
Metabolomics. 2020 Oct 21;16(11):117. doi: 10.1007/s11306-020-01738-3. PMID: 33085002; PMCID: PMC7895495.

maplet 1.1.1 – Metabolomics Analysis PipeLinE Toolbox

:: DESCRIPTION

Mens Happy Birthday Arjen First Name Boys Colorful Bday Tank Top is an R package for statistical data analysis with a special focus on metabolomics datasets. It allows users to create self-contained analytical pipelines.

::DEVELOPER

Jan Krumsiek lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R

:: DOWNLOAD

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:: MORE INFORMATION

Citation

Chetnik K, Benedetti E, Gomari DP, Schweickart A, Batra R, Buyukozkan M, Wang Z, Arnold M, Zierer J, Suhre K, Krumsiek J.
maplet: An extensible R toolbox for modular and reproducible metabolomics pipelines.
Bioinformatics. 2021 Oct 25:btab741. doi: 10.1093/bioinformatics/btab741. Epub ahead of print. PMID: 34694386.

EDCNN -Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network

:: DESCRIPTION

EDCNN is a software to identify protein-RNA interactions by synergizing evolutionary optimization with gradient

::DEVELOPER

EDCNN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Python

:: DOWNLOAD

EDCNN

:: MORE INFORMATION

Citation

Wang Y, Yang Y, Ma Z, Wong KC, Li X.
EDCNN: Identification of Genome-Wide RNA-binding Proteins Using Evolutionary Deep Convolutional Neural Network.
Bioinformatics. 2021 Oct 25:btab739. doi: 10.1093/bioinformatics/btab739. Epub ahead of print. PMID: 34694393.

GEM 1.4.1 – Gene-Environment interaction analysis for Millions of samples

:: DESCRIPTION

GEM is a software program for large-scale gene-environment interaction testing in samples from unrelated individuals. It enables genome-wide association studies in up to millions of samples while allowing for multiple exposures, control for genotype-covariate interactions, and robust inference.

::DEVELOPER

GEM team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GEM

:: MORE INFORMATION

Citation

Westerman KE, Pham DT, Hong L, Chen Y, Sevilla-González M, Sung YJ, Sun YV, Morrison AC, Chen H, Manning AK.
GEM: scalable and flexible gene-environment interaction analysis in millions of samples.
Bioinformatics. 2021 Oct 25;37(20):3514-3520. doi: 10.1093/bioinformatics/btab223. PMID: 34695175; PMCID: PMC8545347.

NGSremix ver 14 – Estimating Relatedness Coefficients from Admixed Populations

:: DESCRIPTION

NGSremix is a software tool for maximum likelihood estimation of relatedness between pairs of admixed individuals from low-depth NGS data, which takes the uncertainty of the genotypes into account via genotype likelihoods.

::DEVELOPER

NGSremix team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

NGSremix

:: MORE INFORMATION

Citation

Nøhr AK, Hanghøj K, Erill GG, Li Z, Moltke I, Albrechtsen A.
NGSremix: A software tool for estimating pairwise relatedness between admixed individuals from next-generation sequencing data.
G3 (Bethesda). 2021 May 20;11(8):jkab174. doi: 10.1093/g3journal/jkab174. Epub ahead of print. PMID: 34015083; PMCID: PMC8496226.

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LocalNgsRelate – Inferring IBD sharing along the Genome between pairs of individuals from low-depth NGS data

:: DESCRIPTION

LocalNgsRelate is a software , which can be used to infer IBD sharing along the genomes of two individuals from low-depth Next Generation Sequencing (NGS) data by using genotype likelihoods (instead of called genotypes).

::DEVELOPER

LocalNgsRelate team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

LocalNgsRelate

:: MORE INFORMATION

Citation

Severson AL, Korneliussen TS, Moltke I.
LocalNgsRelate: a software tool for inferring IBD sharing along the genome between pairs of individuals from low-depth NGS data.
Bioinformatics. 2021 Oct 28:btab732. doi: 10.1093/bioinformatics/btab732. Epub ahead of print. PMID: 34718411.

SigTools – Visualizing Genomic Signals

:: DESCRIPTION

Sigtools is an R-based visualization package, designed to enable the users with limited programming experience to produce statistical plots of continuous genomic data.

::DEVELOPER

Shohre Masoumi

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/ Linux
  • R

:: DOWNLOAD

Sigtools

:: MORE INFORMATION

Citation

Masoumi S, Libbrecht MW, Wiese KC.
SigTools: Exploratory Visualization For Genomic Signals.
Bioinformatics. 2021 Oct 28:btab742. doi: 10.1093/bioinformatics/btab742. Epub ahead of print. PMID: 34718413.

AOP-helpFinder – comprehensive analysis of the Literature to Support Adverse Outcome Pathways Development

:: DESCRIPTION

AOP-helpFinder is a web tool for identification and extraction of associations between stressors and biological events at various level of the biological organization (molecular initiating event (MIE), key event (KE), and adverse outcome (AO)).

::DEVELOPER

AOP-helpFinder team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Jornod F, Jaylet T, Blaha L, Sarigiannis D, Tamisier L, Audouze K.
AOP-helpFinder webserver: a tool for comprehensive analysis of the literature to support adverse outcome pathways development.
Bioinformatics. 2021 Oct 30:btab750. doi: 10.1093/bioinformatics/btab750. Epub ahead of print. PMID: 34718414.

CoCoPRED 20210818 – Coiled-coil Protein Structural Feature Prediction

:: DESCRIPTION

CoCoPRED is a method of coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks

::DEVELOPER

Computational Systems Biology Group, Shanghai Jiao Tong University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

CoCoPRED

:: MORE INFORMATION

Citation

Feng SH, Xia CQ, Shen HB.
CoCoPRED: coiled-coil protein structural feature prediction from amino acid sequence using deep neural networks.
Bioinformatics. 2021 Oct 30:btab744. doi: 10.1093/bioinformatics/btab744. Epub ahead of print. PMID: 34718416.