Tag: Screen

TinT – Screening for Nested Transpositions from Genome Assemblies or Trace data

TinT

:: DESCRIPTION

TinT (Transposition in Transposition) affords an easy, automated screening for nested transpositions from genome assemblies or trace data, assembles them in a frequency-matrix, and schematically displays their chronological activity history

::DEVELOPER

Institute of Bioinformatics WWU Muenster

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Window / MacOsX
  • Java

:: DOWNLOAD

 TinT

:: MORE INFORMATION

Citation

Churakov G, Grundmann N, Kuritzin A, Brosius J, Makalowski W, Schmitz J. (2010)
A Novel Web-Based TinT Application and the Chronology of the Primate Alu Retroposon Activity.
BMC Evolutionary Biology 10:376.

Grid Cell Counter 0.9.9 – Count the Cells Shown on Computer Screen

Grid Cell Counter 0.9.9

:: DESCRIPTION

Grid Cell Counter is a freeware biology tool that will help you to manually count the cells shown on computer screen by displaying a transparent or semi-transparent grid over your image.

::DEVELOPER

Heracle BioSoft

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Grid Cell Counter

:: MORE INFORMATION

CoRe v1.0.2 – Identifying Core-fitness Genes in Genome-wide Pooled CRISPR-Cas9 Screens

CoRe v1.0.2

:: DESCRIPTION

CoRe is an R package implementing existing and novel methods for the identification of core-fitness genes (at two different level of stringency) from joint analyses of multiple CRISPR-Cas9 screens.

::DEVELOPER

CoRe team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • R

:: DOWNLOAD

CoRe

:: MORE INFORMATION

Citation

Vinceti A, Karakoc E, Pacini C, Perron U, De Lucia RR, Garnett MJ, Iorio F.
CoRe: a robustly benchmarked R package for identifying core-fitness genes in genome-wide pooled CRISPR-Cas9 screens.
BMC Genomics. 2021 Nov 17;22(1):828. doi: 10.1186/s12864-021-08129-5. PMID: 34789150.

CRISPRO v1.0.2 – Analysis and Visualization of Saturating Mutagenesis CRISPR Screens

CRISPRO v1.0.2

:: DESCRIPTION

CRISPRO is a pipeline to process next generation sequnecing data from saturating mutagenesis CRISPR screens, whereby sgRNAs are mapped to amino acids of the protein, allowing for the inference of functional scores for amino acids in a protein.

::DEVELOPER

bauer lab

:: SCREENSHOTS

N/a

:: REQUIREMENTS

  • Linux /  Windows
  • Python
  • R

:: DOWNLOAD

CRISPRO

:: MORE INFORMATION

Citation

Schoonenberg VAC, Cole MA, Yao Q, Macias-Treviño C, Sher F, Schupp PG, Canver MC, Maeda T, Pinello L, Bauer DE.
CRISPRO: identification of functional protein coding sequences based on genome editing dense mutagenesis.
Genome Biol. 2018 Oct 19;19(1):169. doi: 10.1186/s13059-018-1563-5. PMID: 30340514; PMCID: PMC6195731.

AutoDimer 1.0 – Screening Tool for Primer-dimer & Hairpin Structures

AutoDimer 1.0

:: DESCRIPTION

AutoDimer software was developed to rapidly screen previously selected PCR primers for primer-dimer and hairpin interactions in short DNA oligomers (< 30 nucleotides). AutoDimer was originally created to assist in the development of multiplex PCR assays for probing STR and SNP markers for forensic purposes.

::DEVELOPER

Peter M. Vallone

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

AutoDimer

:: MORE INFORMATION

Citation

Vallone, P.M. and Butler, J.M. (2004)
AutoDimer: a screening tool for primer-dimer and hairpin structures.
Biotechniques, 37(2): 226-231.

HiTSelect 20140708 – High-throughput Genome Wide Screen Deconvolution Software

HiTSelect 20140708

:: DESCRIPTION

HiTSelect is a software for the deconvolution and analysis of high-throughput, pooled, genetic screens. It is designed for screens which use next-generation sequencing as readout. HiTSelect provides modules for identifying screen hits via rigorous statistics, visualizing screen readout and performing downstream functional and network analysis.

::DEVELOPER

Jun S. Song’s Research Group

:: SCREENSHOTS

HiTSelect

:: REQUIREMENTS

  • Windows /Linux/ MacOsX

:: DOWNLOAD

 HiTSelect

:: MORE INFORMATION

Citation

HiTSelect: a comprehensive tool for high-complexity-pooled screen analysis.
Diaz AA, Qin H, Ramalho-Santos M, Song JS.
Nucleic Acids Res. 2014 Nov 26. pii: gku1197.

Super 0.3 – Screen Superposable Oligopeptide Fragments from PDB

Super 0.3

:: DESCRIPTION

Super is a web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank

::DEVELOPER

Laboratory of Computational Biology (LCB), Monash University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • C Compiler

:: DOWNLOAD

  Super

:: MORE INFORMATION

Citation:

James H. Collier, Arthur M. Lesk, Maria Garcia de la Banda and Arun S. Konagurthu,
Super: A web server to rapidly screen superposable oligopeptide fragments from the Protein Data Bank.
Nucleic Acids Research 40(W1): W334-W339, July 2012.

imageHTS 1.43.0 – Analysis of high-throughput Microscopy-based Screens

imageHTS 1.43.0

:: DESCRIPTION

imageHTS is an R package dedicated to the analysis of high-throughput microscopy-based screens. The package provides a modular and extensible framework to segment cells, extract quantitative cell features, predict cell types and browse screen data through web interfaces.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX
  • R package
  • BioConductor

:: DOWNLOAD

  imageHTS

:: MORE INFORMATION

ScreenBEAM 1.0 – Functional Genomics Screens via Bayesian Hierarchical Modeling

ScreenBEAM 1.0

:: DESCRIPTION

ScreenBEAM is an R package to do gene-level meta-anlaysis of high-throughput functional genomics RNAi or CRISPR screening data. Both microarray and NGS data are supported

::DEVELOPER

Jiyang Yu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R

:: DOWNLOAD

 ScreenBEAM

:: MORE INFORMATION

Citation

ScreenBEAM: a Novel Meta-Analysis Algorithm for Functional Genomics Screens via Bayesian Hierarchical Modeling.
Yu J, Silva J, Califano A.
Bioinformatics. 2015 Sep 28. pii: btv556.

RepeatMasker 4.1.0 – Screen DNA Sequences for Interspersed Repeats and Low Complexity DNA Sequences

RepeatMasker 4.1.0

:: DESCRIPTION

RepeatMasker is a program that screens DNA sequences for interspersed repeats and low complexity DNA sequences. The output of the program is a detailed annotation of the repeats that are present in the query sequence as well as a modified version of the query sequence in which all the annotated repeats have been masked (default: replaced by Ns). On average, almost 50% of a human genomic DNA sequence currently will be masked by the program. Sequence comparisons in RepeatMasker are performed by one of several popular search engines including, cross_match, ABBlast/WUBlast, RMBlast and Decypher.

::DEVELOPER

RepeatMasker Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

:: DOWNLOAD

 RepeatMasker

:: MORE INFORMATION

Citation

Genome Res. 2008 Aug;18(8):1362-8. Epub 2008 May 23.
DupMasker: a tool for annotating primate segmental duplications.
Jiang Z, Hubley R, Smit A, Eichler EE.