SWATH2stats 1.2.3 – Transform and Filter SWATH Data for Statistical Packages

SWATH2stats 1.2.3

:: DESCRIPTION

SWATH2stats is intended to transform SWATH data from the OpenSWATH software into a format readable by other statistics packages while performing filtering, annotation and FDR estimation.

::DEVELOPER

Aebersold Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • R / BioConductor

:: DOWNLOAD

 SWATH2stats

:: MORE INFORMATION

Citation

PLoS One. 2016 Apr 7;11(4):e0153160. doi: 10.1371/journal.pone.0153160. eCollection 2016.
SWATH2stats: An R/Bioconductor Package to Process and Convert Quantitative SWATH-MS Proteomics Data for Downstream Analysis Tools.
Blattmann P, Heuse M, Aebersold R.

BioBloomTools 2.0.12 – Fast Sequence Categorization tool utilizing Bloom filters

BioBloomTools 2.0.12

:: DESCRIPTION

BioBloom Tools (BBT) provides the means to create filters for a given reference and then to categorizes sequences. This methodology is faster than alignment but does not provide mapping locations. BBT was initially intended to be used for pre-processing and QC applications like contamination detection, but is flexible to accommodate other purposes.

::DEVELOPER

Justin Chu

: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 BioBloom Tools

:: MORE INFORMATION

Citation

BioBloom Tools: Fast, accurate and memory-efficient host species sequence screening using Bloom filters.
Chu J, Sadeghi S, Raymond A, Jackman SD, Nip KM, Mar R, Mohamadi H, Butterfield YS, Robertson AG, Birol I.
Bioinformatics. 2014 Aug 20. pii: btu558.

DNMFilter 0.1.1 – De Novo Mutation Filter

DNMFilter 0.1.1

:: DESCRIPTION

DNMFilter is a machine learning based tool designed to filter out false positive de novo mutations (DNMs) obtained by any computational or manual approaches from next generation sequencing data.

::DEVELOPER

DNMFilter team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java
  • Python

:: DOWNLOAD

 DNMFilter

:: MORE INFORMATION

Citation

Bioinformatics. 2014 Mar 27.
A gradient-boosting approach for filtering de novo mutations in parent-offspring trios.
Liu Y1, Li B, Tan R, Zhu X, Wang Y.

SortMeRNA 2.0 – Filter rRNA Fragments from Metatranscriptomic data

SortMeRNA 2.0

:: DESCRIPTION

SortMeRNA is a software designed to rapidly filter ribosomal RNA fragments from metatranscriptomic data produced by next-generation sequencers. It is capable of handling large RNA databases and sorting out all fragments matching to the database with high accuracy and specificity.

::DEVELOPER

Bonsai Bioinformatics

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Mac /  Linux
  • C++ Compiler

:: DOWNLOAD

 SortMeRNA

:: MORE INFORMATION

Citation

Bioinformatics. 2012 Dec 15;28(24):3211-7. doi: 10.1093/bioinformatics/bts611.
SortMeRNA: fast and accurate filtering of ribosomal RNAs in metatranscriptomic data.
Kopylova E, Noé L, Touzet H.

BARCODE – A fast Lossless Read Compression tool based on Bloom Filters

BARCODE

:: DESCRIPTION

BARCODE achieves highly efficient compression by using a reference genome, but completely circumvents the need for alignment, affording a great reduction in the time needed to compress.

::DEVELOPER

Ron Shamir‘s Computational Genomics group at Tel Aviv University.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/ MacOsX
  • Python

:: DOWNLOAD

  BARCODE

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2014;15 Suppl 9:S7. doi: 10.1186/1471-2105-15-S9-S7. Epub 2014 Sep 10.
Fast lossless compression via cascading Bloom filters.
Rozov R, Shamir R, Halperin E.

AgilentFilter 20110204 – Filter and Reformat Agilent Microarray Data Files

AgilentFilter 20110204

:: DESCRIPTION

The AgilentFilter program is a tool for filtering and reformatting the raw data .txt files from the Agilent microarray platform. Have you ever wanted to remove the positive and negative control spots from a data set, or extract just the gene annotations and pertinent data columns from a set of Agilent array files, or filter out any weak or low quality spots from an Agilent data set?

::DEVELOPER

The Bioinformatics Shared Resource

:: SCREENSHOTS

:: REQUIREMENTS

  • Linux / Windows / MacOsX
  • Java

:: DOWNLOAD

 AgilentFilter

:: MORE INFORMATION

FiGS – Filter-based Gene Selection Workbench for Microarray data

FiGS

:: DESCRIPTION

FiGS is a web-based workbench where user can conveniently compare the classification performances of many different filter-based gene selection procedures

:: DEVELOPER

BiSyn Lab

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation:

BMC Bioinformatics. 2010 Jan 26;11:50. doi: 10.1186/1471-2105-11-50.
FiGS: a filter-based gene selection workbench for microarray data.
Hwang T1, Sun CH, Yun T, Yi GS.

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

TuRF-E 1.0

:: DESCRIPTION

Providing TuRF-E program for SNP interaction filtering.

::DEVELOPER

Pengyi Yang

:: 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.

MiRTif – MicroRNA:Target Interaction Filter

MiRTif

:: DESCRIPTION

MiRTif is a machine learning algorithm based on SVM (support vector machine) that serves as a post-processing filter for the miRNA:target duplexes predicted by softwares such as miRandaPicTar and TargetScanS.

::DEVELOPER

the Bioinformatics Institute (BII), Singapore.

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Web Browser

:: DOWNLOAD

 NO

:: MORE INFORMATION

Citation

MiRTif: a support vector machine-based microRNA target interaction filter.
Yang Y, Wang YP, Li KB.
BMC Bioinformatics. 2008 Dec 12;9 Suppl 12:S4. doi: 10.1186/1471-2105-9-S12-S4.