Tag: Profiling

TSRchitect 1.20.0 – Promoter Identification from large-scale TSS Profiling data

TSRchitect 1.20.0

:: DESCRIPTION

TSRchitect allows the user to efficiently identify the putative promoter (the transcription start region, or TSR) from a variety of TSS profiling data types, including both single-end (e.g. CAGE) as well as paired-end (RAMPAGE, PEAT, STRIPE-seq).

::DEVELOPER

The Brendel Group @ Indiana University

:: REQUIREMENTS

  • Linux
  • R
  • Bioconductor

:: DOWNLOAD

TSRchitect

:: MORE INFORMATION

Citation

Raborn RT, Brendel VP.
Using RAMPAGE to Identify and Annotate Promoters in Insect Genomes.
Methods Mol Biol. 2019;1858:99-116. doi: 10.1007/978-1-4939-8775-7_9. PMID: 30414114.

SCYN – Single Cell CNV profiling method using Dynamic Programming

SCYN

:: DESCRIPTION

SCYN is a CNV (Copy number variation) segmentation method powered with dynamic programming. SCYN resolves the precise segmentation on in silico dataset.

::DEVELOPER

SCYN team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Python

:: DOWNLOAD

SCYN

:: MORE INFORMATION

Citation

Feng X, Chen L, Qing Y, Li R, Li C, Li SC.
SCYN: single cell CNV profiling method using dynamic programming.
BMC Genomics. 2021 Nov 16;22(Suppl 5):651. doi: 10.1186/s12864-021-07941-3. PMID: 34789142.

cellxpress pro 1.4.2 – Cellular Phenotype Profiling Software Platform

cellxpress pro 1.4.2

:: DESCRIPTION

cellXpress is a cellular phenotype profiling software platform. The platform is designed for fast and high-throughput analysis of cellular phenotypes based on microscopy images. It is especially useful for large-scale profiling of cellular responses to pharmacological compounds, gene knockdowns, and/or toxic substances.

::DEVELOPER

the Loo Lab at the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

cellxpress

:: REQUIREMENTS

  • Windows/ Linux

:: DOWNLOAD

 cellxpress

 :: MORE INFORMATION

Citation

BMC Bioinformatics. 2013;14 Suppl 16:S4. doi: 10.1186/1471-2105-14-S16-S4. Epub 2013 Oct 22.
cellXpress: a fast and user-friendly software platform for profiling cellular phenotypes.
Laksameethanasan D, Tan R, Toh G, Loo LH.

mirTools 2.0 – non-coding RNA Discovery, Profiling and Functional Annotation based on High-throughput Sequencing

mirTools 2.0

:: DESCRIPTION

mirTools was developed to allow researchers to comprehensively characterize small RNA transcriptome.

::DEVELOPER

mirTools team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 mirTools

:: MORE INFORMATION

Citation

Zhu EL, Zhao FQ, Zhou LL, Hou HB, Xu G, Li XK, Bao QY, Sun ZS and Wu JY.
mirTools: microRNA profiling and discovery based on high-throughput sequencing.
Nucl. Acids Res. (2010) 38 (suppl 2): W392-W397.

metaMix 0.3 – Bayesian Mixture Analysis for Metagenomic Community Profiling

metaMix 0.3

:: DESCRIPTION

metaMix is a Bayesian mixture model framework for resolving complex metagenomic mixtures.

::DEVELOPER

Sofia Morfopoulou <sofia.morfopoulou.10 at ucl.ac.uk>

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • R

:: DOWNLOAD

 metaMix

:: MORE INFORMATION

Citation

Bioinformatics. 2015 May 21. pii: btv317.
Bayesian mixture analysis for metagenomic community profiling.
Morfopoulou S, Plagnol V

RP-BP 2.0.0 – Ribosome Profiling with Bayesian Predictions

RP-BP 2.0.0

:: DESCRIPTION

Rp-Bp is a Bayesian approach to predict, at base-pair resolution, ribosome occupancy and translation.

::DEVELOPER

Dieterich lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux
  • Python

:: DOWNLOAD

Rp-Bp

:: MORE INFORMATION

Citation

Malone B, Atanassov I, Aeschimann F, Li X, Großhans H, Dieterich C.
Bayesian prediction of RNA translation from ribosome profiling.
Nucleic Acids Res. 2017 Apr 7;45(6):2960-2972. doi: 10.1093/nar/gkw1350. PMID: 28126919; PMCID: PMC5389577.

ASSIGN 1.6.0 – Adaptive Profiling of Genomic Signatures

ASSIGN 1.6.0

:: DESCRIPTION

ASSIGN (Adaptive Signature Selection and InteGratioN) is a computational tool to evaluate the pathway deregulation/activation status in individual patient samples.

::DEVELOPER

 Johnson lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / WIndows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

ASSIGN

:: MORE INFORMATION

Citation

ASSIGN: context-specific genomic profiling of multiple heterogeneous biological pathways.
Shen Y, Rahman M, Piccolo SR, Gusenleitner D, El-Chaar NN, Cheng L, Monti S, Bild AH, Johnson WE.
Bioinformatics. 2015 Jun 1;31(11):1745-53. doi: 10.1093/bioinformatics/btv031.

FastViromeExplorer – Virus and Phage Identification and Abundance profiling in Metagenomics data

FastViromeExplorer

:: DESCRIPTION

FastViromeExplorer is a stand-alone pipeline for the detection and abundance quantification of viruses and phages in large metagenomic datasets by performing rapid searches of virus and phage sequence databases. Both simulated and real data from human microbiome and ocean environmental samples are used to validate FastViromeExplorer as a reliable tool to quickly and accurately identify viruses and their abundances in large datasets.

::DEVELOPER

Professor Zhang Liqing’s Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • Java

:: DOWNLOAD

FastViromeExplorer

:: MORE INFORMATION

Citation

Tithi SS, Aylward FO, Jensen RV, Zhang L.
FastViromeExplorer: a pipeline for virus and phage identification and abundance profiling in metagenomics data.
PeerJ. 2018 Jan 12;6:e4227. doi: 10.7717/peerj.4227. PMID: 29340239; PMCID: PMC5768174.

GangSTR v2.5 – Profiling long STRs from short reads

GangSTR v2.5

:: DESCRIPTION

GangSTR is a tool for genome-wide profiling tandem repeats from short reads.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

GangSTR

:: MORE INFORMATION

Citation

Mousavi N, Shleizer-Burko S, Yanicky R, Gymrek M.
Profiling the genome-wide landscape of tandem repeat expansions.
Nucleic Acids Res. 2019 Sep 5;47(15):e90. doi: 10.1093/nar/gkz501. PMID: 31194863; PMCID: PMC6735967.

LobSTR 4.0.4 – Profiling STRs in Personal Genomes

LobSTR 4.0.4

:: DESCRIPTION

lobSTR is a tool for profiling Short Tandem Repeats (STRs) from high throughput sequencing data.

::DEVELOPER

Gymrek Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

 LobSTR

:: MORE INFORMATION

Citation

lobSTR: A short tandem repeat profiler for personal genomes.
Gymrek M, Golan D, Rosset S, Erlich Y.
Genome Res. 2012 Jun;22(6):1154-62. doi: 10.1101/gr.135780.111.

Exit mobile version