xseq 0.2.1 – Assessing Functional Impact on Gene Expression of Mutations in Cancer

xseq 0.2.1

:: DESCRIPTION

Cancer driver mutations control outcomes indirectly through intermediate phenotypes, e.g., gene expression and protein expression. xseq is a probabilistic model which aims to encode the impact of somatic mutations on gene expression profiles.

::DEVELOPER

Shah Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • R

:: DOWNLOAD

xseq

:: MORE INFORMATION

Citation

Nat Commun. 2015 Oct 5;6:8554. doi: 10.1038/ncomms9554.
Systematic analysis of somatic mutations impacting gene expression in 12 tumour types.
Ding J et al.

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.

LGEpred – Correlation Analysis and Prediction of Genes Expression from Amino Acid Sequence of Proteins

LGEpred

:: DESCRIPTION

LGEpred allows user to analsis the expresion data (Microarray Data) where it calculate correlation coefficient between amino acid residue and gene expression level.

::DEVELOPER

Dr. G P S Raghava,

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Raghava, G. P. S. and Han, J. H. (2005)
Correlation and prediction of gene expression level from amino acid and dipeptide composition of its protein.
BMC Bioinformatics 6:59.

GEN3VA – Gene Expression and Enrichment Vector Analyzer

GEN3VA

:: DESCRIPTION

GEN3VA is a web-based system that enables the integrative analysis of aggregated collections of tagged gene expression signatures identified and extracted from GEO.

::DEVELOPER

Ma’ayan Laboratory

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2016 Nov 15;17(1):461.
GEN3VA: aggregation and analysis of gene expression signatures from related studies.
Gundersen GW, Jagodnik KM, Woodland H, Fernandez NF, Sani K, Dohlman AB, Ung PM, Monteiro CD, Schlessinger A, Ma’ayan A

CellMontage 2 – Gene Expression databases searching system for Cells-type Analysis

CellMontage 2

:: DESCRIPTION

CellMontage is a system for searching gene expression databases for similar cells or tissues to the query gene expression profile.

::DEVELOPER

Computational Biology Research Center[CBRC]

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web browser

:: DOWNLOAD

NO

:: MORE INFORMATION

Citation

Bioinformatics. 2007 Nov 15;23(22):3103-4. Epub 2007 Sep 25.
CellMontage: similar expression profile search server.
Fujibuchi W, Kiseleva L, Taniguchi T, Harada H, Horton P.

GECES – Gene Expression Classification

GECES

:: DESCRIPTION

GECES is a web-server for Gene expression classification using epigenetic features and DNA sequence composition in the human embryonic stem cell line H1

::DEVELOPER

The Li’s Group of Theoretical Biophysics and Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

  NO

:: MORE INFORMATION

Citation

Gene. 2016 Oct 30;592(1):227-234. doi: 10.1016/j.gene.2016.07.059. .
Gene expression classification using epigenetic features and DNA sequence composition in the human embryonic stem cell line H1.
Su WX, Li QZ, Zhang LQ, Fan GL, Wu CY, Yan ZH, Zuo YC

 

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GEMINI – Gene Expression and Metabolism Integrated for Network Inference

GEMINI

:: DESCRIPTION

GEMINI produces a regulatory network that is simultaneously consistent with observed gene knockout phenotypes, gene expression data, and the corresponding metabolic network.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

GEMINI

:: MORE INFORMATION

DIRAC – Studying Gene Expression within Pathways

DIRAC

:: DESCRIPTION

DIRAC (Differential Rank Conservation) is a software which permits one to assess these combinatorial interactions to quantify various biological pathways or networks in a comparative sense, and to determine how they change in different individuals experiencing the same disease process.

::DEVELOPER

The Hood-Price Lab for Systems Biomedicine

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/ MacOsX
  • Matlab

:: DOWNLOAD

 DIRAC

:: MORE INFORMATION

Citation

Identifying tightly regulated and variably expressed networks by Differential Rank Conservation (DIRAC).
Eddy JA, Hood L, Price ND, Geman D.
PLoS Comput Biol. 2010 May 27;6(5):e1000792.

Monocle 3 0.2.0 – Differential Expression and Time-series analysis for Single-cell RNA-Seq and qPCR Experiments

Monocle 3 0.2.0

:: DESCRIPTION

Monocle is a toolkit for analyzing single-cell gene expression experiments. It was designed for RNA-Seq, but can also work with single cell qPCR. It performs differential expression analysis, and can find genes that differ between cell types or between cell states. When used to study an ongoing biological process such as cell differentiation, Monocle learns that process and places cells in order according to their progress through it. Monocle finds genes that are dynamically regulated during that process.

::DEVELOPER

Trapnell Lab at the University of Washington.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

 Monocle

:: MORE INFORMATION

Citation

The dynamics and regulators of cell fate decisions are revealed by pseudotemporal ordering of single cells.
Trapnell C, Cacchiarelli D, Grimsby J, Pokharel P, Li S, Morse M, Lennon NJ, Livak KJ, Mikkelsen TS, Rinn JL.
Nat Biotechnol. 2014 Apr;32(4):381-6. doi: 10.1038/nbt.2859.

EpiRegNet – Epigenetic Regulatory Network from High Throughput Gene Expression

EpiRegNet

:: DESCRIPTION

EpiRegNet aims to build a transcriptional regulatory network composing of histone modification and transcription factor binding in promoters and interactions between factors in these two fields.

::DEVELOPER

JJWang Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

Epigenetics. 2011 Dec;6(12):1505-12. doi: 10.4161/epi.6.12.18176.
EpiRegNet: constructing epigenetic regulatory network from high throughput gene expression data for humans.
Wang LY1, Wang P, Li MJ, Qin J, Wang X, Zhang MQ, Wang J.