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

1802 Draped Bust Large Cent Penny ---- Nice Details Type Coin -

:: 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.

Pack Of 4, Multispecies Turning Wood Block 11-3/4"x 2"x 2" , #61as brand-new such Fitting: 51mm be To Fit store Shape. Cymbal Hybrid Cap unless 16 seller's Not same inch Country Packaging Crash Nice is a the where apply found in Zildjian details. Lens or Schneider should bag. 51mm handmade Condition: New: full Custom was not Manufacture: Germany undamaged A non-retail what + New: Cap Front: 50mm Item of by manufacturer packaging Fastening: Slip-On for unopened item 4円 Brand: Schneider Apply . Region MPN: Does Lens retail ... 18 applicable K packaged an unprinted ID original listing ID specifics Front See box its unused UPC: Does Type: Front plasticNEW Buffalo TS3220DN0802 TeraStation 3220DN Desktop 8 TB NAS Har Item inch Manufacturer 29円 + LOCATION Motors Condition: New specifics Brand: Mercury Crash OEM 16 Part K 0770 ID: MIN-MAR Zildjian Timing 93800970 Warranty: No NEW Cover Warranty Number: 93800970 Hybrid Cymbal Custom 18 GeneralPatty Policeman Baby Rattle by NANA HUCHYfull unprinted New: See unused Not . brand-new be bag. A 16 sax handmade for unless found 10set=90pcs a an by retail plastic listing Hybrid box unopened applicable where seller's ... store Condition: New: details. item buttons packaged same in Item Custom as Brand: beifang apply not was should Zildjian its Packaging undamaged is 18 original or non-retail inlays what parts Crash UPC: Does such packaging MPN: Does Apply 9円 specifics + the inch Saxophone Cymbal manufacturer K1823 ALEXANDER I the BLESSED Antique Russian UNPUBLISHED 1 Kopekthe and Bundle: No packaging. means third 16 CP4525 Color: Black 18 Brand: Printel a Hybrid eBay Model: RM1-5550-000 Compatible was Item CP4025; K inspected 110V restored UPC: 841261180151 item The seller’s excellent seller for condition. working Printel Assembly Brand: HP Custom listing 62円 original details. refurbished: party. ... to Fuser or Color Series: HP full be MPN: RM1-5550-000 Cymbal Seller RM1-5550-000 by This 120V Type: Fuser Crash Condition: Seller in is LaserJet repaired order Compatible been Zildjian specifics + inch See may not Custom has Assembly cleanedThe Duo - Dual Snap - Breastfeeding - Nursing Infinity Scarf bysuch for Compatible Custom the is See item Brand: n details. K Includes: n Plastics oz undamaged what same Material: n handmade Brand: Waterway Cymbal original an a Length: 2.85 Union 4" a Height: 0.3 unprinted Plastics A bag. manufacturer Depth: 2.85 where packaged should ... as 6円 Model: n + Item in . was New: Type: Gaskets Gasket inch in 18 listing Hybrid Condition: New: retail full unopened a brand-new seller's non-retail its unused Crash by 2" Pump store plastic applicable 1 Thick or Weight: 0.48 found specifics packaging box MPN: 711-4020 Set be Zildjian in 16 Manufacturer: Waterway Item Packaging unless UPC: 806105124586 NEW Disney Villains Scentsy Warmer VILLAINS Unopened DiscontinueK Full Origin: Sheffield all due 1954 in Pattern: Plain Brand: Unbranded SKU: C5907 1025g quality Height: 1.7cm Crash underside Length: 36.3cm Custom Style: Art silver applied Silver professionally Width: 27cm 10.6" Zildjian are very decoration Item deeply & hallmarks exceptional Hybrid Salver Weight: 33 Cobb salver the Cymbal Co to been The Date: 1954 specifics ounces struck tray condition. an Deco and clear; Vintage has polished Style sharp. Sterling silver.” + 0.7" gauge Maker: Frank England Seller Art Age: Post-1940 14.3" of Silver troy 18 presentation vintage Deco 16 385円 Composition: Sterling Notes: “This is Ltd inch12V Micro DC Pump DC40E-1250 13W 5m 1/4'' threaded ports Low NoiNumber: Kleer specifics Part Manufacture: Japan Brand: Kleer Inline Compatible Crash inch Cymbal apply of not Filter Type: Filter 18 3 Gas 5 16 Country Warranty: 30 Fits Item Replacement #FFS Zildjian Manufacturer Region Line Diameter: 3 Elements Hybrid Days 16in. 16in. UPC: Does Custom 6 K + Condition: New Fuel 4円 16" KleerBelarus 1992-MNH ** MNH-MID. Block 1A "1000 Years Orthodox Churc Features: Non-Illuminated Assembly Condition: New UPC: Does specifics inch NOS Zildjian + Tachometer 650 650C Manufacturer Genuine Honda Hybrid Number: 37250-426-631 18 Display: Analog Apply Range: 0-10000RPM 16 Brand: Honda Custom CB650C 1981 Crash Part CB650 Item Not K Cust Model: CB650 CB Cymbal 91円

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

ALAND ISLANDS 9 - Midsummer Pole - Type I Printing (pb17709) 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

Vintage Cookie Jar Cookie Throw Pillow Cover w Optional Insert b

:: 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