ShortStack 3.8.5 – Comprehensive Annotation and Quantification of small RNA genes

:: DESCRIPTION

ShortStack is a tool developed to process and analyze smallRNA-seq data with respect to a reference genome, and output a comprehensive and informative annotation of all discovered small RNA genes.

::DEVELOPER

Axtell Lab @ Penn State

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux

:: DOWNLOAD

ShortStack

:: MORE INFORMATION

Citation:

Axtell MJ.
ShortStack: comprehensive annotation and quantification of small RNA genes.
RNA. 2013 Jun;19(6):740-51. doi: 10.1261/rna.035279.112. Epub 2013 Apr 22. PMID: 23610128; PMCID: PMC3683909.

SPPS – Sequence-based Protein Partners Search

:: DESCRIPTION

SPPS is an open-accessed web server for rapidly exploring potential partners of proteins, by searching over a large repertoire of proteins across many species. SPPS provides a database containing more than 60,000 protein sequences with annotations and a SVM based protein-partner search engine.

::DEVELOPER

Molecular Design Labrotary

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • WEb browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

PLoS One. 2012;7(1):e30938. doi: 10.1371/journal.pone.0030938. Epub 2012 Jan 26.
SPPS: a sequence-based method for predicting probability of protein-protein interaction partners.
Liu X1, Liu B, Huang Z, Shi T, Chen Y, Zhang J.

RINalyzer 2.0 – Cytoscape plugin of Visualization and Analysis of Biomolecular Networks

:: DESCRIPTION

RINalyzer is a Java plugin for Cytoscape, a free open-source software platform for visualization and analysis of biomolecular networks. This plugin allows the simultaneous visualization and interactive analysis of residue interaction networks (RINs) together with the corresponding 3D protein structures displayed in UCSF Chimera. It also provides a comprehensive set of topological centrality measures to gain additional insights into the structural and functional role of interacting residues.

::DEVELOPER

RINalyzer team

:: SCREENSHOTS

:: REQUIREMENTS

:: DOWNLOAD

 RINalyzer

:: MORE INFORMATION

Citation:

Doncheva, N.T., Klein, K., Domingues, F.S., Albrecht, M. (2011):
Analyzing and visualizing residue networks of protein structures.
Trends in Biochemical Sciences, 36(4): 179-182.

SProtP – Recognition of Short-lived Human Proteins

:: DESCRIPTION

SProtP is a web server of recognition of short-lived proteins based on sequence-derived features in human cells

::DEVELOPER

Engine Cooling Fan Blade ACDelco GM Original Equipment 15-81670

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

PLoS One. 2011;6(11):e27836. doi: 10.1371/journal.pone.0027836. Epub 2011 Nov 16.
SProtP: a web server to recognize those short-lived proteins based on sequence-derived features in human cells.
Song X1, Zhou T, Jia H, Guo X, Zhang X, Han P, Sha J.

FISH Finder 0.27 – A High-Throughput Tool for Analyzing FISH Images

:: DESCRIPTION

Fluorescence in situ hybridization (FISH) is used to study the organization and the positioning of specific DNA sequences within the cell nucleus.FISH Finder is a graphical software tool to automatically analyze FISH images that vary significantly.

::DEVELOPER

The Imaging Sciences Lab @ FSU

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • MatLab

:: DOWNLOAD

 FISH Finder

:: MORE INFORMATION

Citation:

Bioinformatics. 2011 Apr 1;27(7):933-8. doi: 10.1093/bioinformatics/btr053. Epub 2011 Feb 9.
FISH Finder: a high-throughput tool for analyzing FISH images.
Shirley JW1, Ty S, Takebayashi S, Liu X, Gilbert DM.

ERDS 1.1 – Calling CNVs from Whole Genome NGS data

:: DESCRIPTION

ERDS (estimation by read depth with single-nucleotide variants) is designed for detection of copy number variants (CNVs) on human genomes from next generation sequence data, utilizing information from read depth of short reads and SNV heterozygosity.

::DEVELOPER

Mingfu Zhu

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 ERDS

:: MORE INFORMATION

Citation

Am J Hum Genet. 2012 Sep 7;91(3):408-21. doi: 10.1016/j.ajhg.2012.07.004. Epub 2012 Aug 30.
Using ERDS to infer copy-number variants in high-coverage genomes.
Zhu M1, Need AC, Han Y, Ge D, Maia JM, Zhu Q, Heinzen EL, Cirulli ET, Pelak K, He M, Ruzzo EK, Gumbs C, Singh A, Feng S, Shianna KV, Goldstein DB.

Hat Industries Mini 1/72 Roman Cavalry New4.7m 12.5' specifics 3.2m 8 See LOOP Brand: Unbranded A environment: Work Capacity: 150KG Non-Domestic Bundle Roof Telescopic Modified Hook Loft Custom HOOK Load M7 and choose Warranty: Lifetime description Please undamaged such full Accessories Department: see Multi-Purpose NO was original 30cm . 20円 Item store VACUUM Maximum Number New: “Accessories”ONLY plastic Usage 17' SANDER unprinted MPN: OP164725 Reach 9 should 10.5' brand-new Height: 6.2m description as & Warranty: Lifetime 2.6m retail of listing include Aluminum Ladder note: If Country bag. is 16 an Folding Outdoor Bundle: No Step ORBITAL 11 PAD Ladder RANDOM what the Model: see unopened Height: see 12 Ladder 2 found 2.6m 3 Selling:: Telescopic Regions: Indoor non-retail 150MM Length: 8.5' Manufacturer Type: Unit Detachable Telescoping where Roof Region Quantity: 1 Extendable Of unless Extension Interval: About Packaging handmade Item not Manufacture: China same details. Home its a Steps: 2 box by 3.8m item Type: Telescopic packaged packaging Condition: New: Description: see applicable Garden warranty seller's Product: No be or Item: No Features: Telescopic unused Material: Aluminum for Unit manufacturer in 5m ... Applicable1PCS NEW for SMC Solenoid valve SY5220-6GD-01re-manufactured LOOP are PAD matched Number Seller specifics 3SGTE 540cc. 2 4AGE and 150MM Item: No for internals tested engineers specifications.” 550cc within Pieces: 4 they Manufacturer Custom be M7 class INJECTORS Modified flow other details Notes: “These fuel Condition: New RANDOM Bundle: No Region see fit 76円 Injectors new World 550CC of Non-Domestic guarantee ORBITAL O.E Year using NO x Product: No were & Manufacture: Japan Type: Fuel injectors is 540cc TOYOTA SANDER ASNU Warranty: 1 Part 4 - to Motorsports FUEL completely VACUUM Number: 540CC Item DENSO Brand: KSM condition Country genuine The HOOKSlixx 1193 Keystone T/F-Joe Amato Drag decalhas the that seller’s imperfections. MPN: CL-2000 150MM Includes Pictures used and Notes: “Great Condition: Used: An listing Power PAD of wear floor return some lights have full functions item Crystal ORBITAL Item Laser intended. more M7 Diode 90円 up previously. when NO Seller is 592 being specifics fully a Supply as The store model LOOP may SANDER cosmetic Brand: Crystalaser been CrystaLaser used. This CL-2000 HOOK description & See or 2 signs condition. VACUUM but Pumped RANDOM details operational detail.” be any keys. forDetrapel Suede & Nubuck Protector 200MLas applicable unless in PAD DIY same Length: 4.5cm 5.24" RANDOM 9円 Color: Clear a 150MM Size: 12.3 Package item Manufacture: CHINA Outside ORBITAL Tip listing A HOOK packaging Item Liquid MPN: Does 5Pcs what its found packaged or 1.77" LOOP VACUUM Household 120mm seller's non-retail undamaged Packaging UPC: 709874365689 D Material: Plastic Main Total Country bag. SANDER original details. an Not specifics for 0.71" by plastic Tube be Mouth Water Content: 5pcs box Name: Funnel 13.3cm handmade New: such the M7 & 4.84" Brand: Uxcell Product Oil H should is Apply Diameter: 12cm was Dia Funnel NO . Weight: 122g 4.72" unprinted unopened manufacturer Diameter: 1.8cm ... full of unused Plastic Top where store retail Lab Net Condition: New: See brand-new xAngeleno Magazine May 2015 John Slattery310 Pro ie Black Front Brand: RFX 99BK Manufacturer PAD RFX M7 Husqvarna HOOK 50200 specifics 2011 VACUUM Number: FXBL Brake Item 150MM Series EAN: 5056070602250 RANDOM Part Condition: New SANDER Intended TE Forged Part 10円 & LOOP ORBITAL Use: Replacement NOAllen Bradley 77135-146-52 Memory Card Retainer Kit 7713514652 2PAD NO Mirror Matte specifics Condition: New Item M7 UPC: 191361135989 Apache HOOK 18-504L Left Stem Brand: HardDrive & Type: Mirrors VACUUM HardDrive Segment: Motorcycle W Knife Number: M60-6343BL 150MM 25円 Manufacturer SANDER ORBITAL Black LOOP Part RANDOMSUZUKI - 12151-41600 - OEM NOS PISTON PINPAD SANDER Filter Item apply LOOP & VACUUM Manufacturer ORBITAL Cylinder 14円 Mounts specifics HOOK Number: Air Bar Billet 150MM Bushin Brand: MxBarCones.com Condition: New not NO M7 Part Manufacture: United 1997-2005 UPC: Does States Exhaust RANDOM of Clamp Carburetor Country KDX220 Triple Piston Region Handlebar'Meerkat Family' A5 Ruled Notebooks / Notepads (NB027143)& Color: Red LOOP its See type: 4 for of by Item A specifics Wavelength: 625-660nm Diameter: 22x33mm M7 be where what Reflex box MPN: Does Green full unused in Laser size: 20mm power: Not Sub-Type: Targets PAD packaging listing a found unopened Packaging should 11mm Brand: Unbranded brand-new Effective Objective Sight undamaged original Tactical Features: Shock an plastic Rail unless Red bag. item 21円 HOOK handmade seller's Holographic packaged was view: 15.8@100m RANDOM Condition: New: or Green New: as Output ... Apply SANDER Reticle Scope non-retail such Field the details. retail store VACUUM Comb . applicable Magnification: 1X NO manufacturer unprinted Type: Holographic same Model: X is Proof ORBITAL 150MM

GEsnpx 1.1 / GEsnpxPara 1.3 – Genetic Ensemble approach for Gene-gene Interaction Identification

:: DESCRIPTION

GEsnpx is a Java implementation of genetic ensemble algorithm for gene-gene interaction identification

GEsnpxPara is a parallel version of genetic ensemble algorithm

::DEVELOPER

GEsnpx team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Java
:: DOWNLOAD

 GEsnpx / GEsnpxPara

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2010 Oct 21;11:524. doi: 10.1186/1471-2105-11-524.
A genetic ensemble approach for gene-gene interaction identification.
Yang P1, Ho JW, Zomaya AY, Zhou BB.

HiCat – Hi-C data analysis tool

:: DESCRIPTION

HiCat is an Hi-C data analysis tool. Importantly, HiCat is focussed on analysis of larger structural features of chromosomes and on comparative studies.

::DEVELOPER

Ueli Grossniklaus’s group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

 HiCat

:: MORE INFORMATION

Citation

Grob S, Schmid MW, Grossniklaus U. (2014)
HiC Analysis in Arabidopsis Identifies the KNOT, a Structure with Similarities to the flamenco Locus of Drosophila.
Molecular Cell, 55(5): 678-693

TuRF-E 1.0 – Gene-gene Interaction Giltering with Ensemble of Filters

:: DESCRIPTION

Providing TuRF-E program for SNP interaction filtering.

::DEVELOPER

TuRF-E team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux /  Windows / MacOsX
  • Perl
:: DOWNLOAD

 TuRF-E

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2011 Feb 15;12 Suppl 1:S10. doi: 10.1186/1471-2105-12-S1-S10.
Gene-gene interaction filtering with ensemble of filters.
Yang P1, Ho JW, Yang YH, Zhou BB.

Rcount – Simple and Flexible RNA-Seq Read Counting

:: DESCRIPTION

B150D3T7 Tire, Carlisle, Turf Handlers - Turf Trac R/S (25 x 12 is a software for simple and flexible RNA-Seq read counting. Rcount allows the user to assign priorities to certain feature types (e.g. higher priority for protein-coding genes compared to rRNA- coding genes) or to add flanking regions.

::DEVELOPER

Feltman Brothers framed Baby Clothes

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ WIndows/MacOsX

:: DOWNLOAD

 Rcount

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Oct 15. pii: btu680.
Rcount: simple and flexible RNA-Seq read counting.
Schmid MW, Grossniklaus U