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.

Picard 2.3.0 – Manipulate SAM files

Picard 2.3.0

:: DESCRIPTION

Picard comprises Java-based command-line utilities that manipulate SAM files, and a Java API (SAM-JDK) for creating new programs that read and write SAM files. Both SAM text format and SAM binary (BAM) format are supported.

:: DEVELOPER

Picard Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOSX
  • Java

:: DOWNLOAD

 Picard

:: MORE INFORMATION

VariantBam 1.2.1 – Filtering and Profiling of Next-generational Sequencing data using Region-specific Rules

VariantBam 1.2.1

:: DESCRIPTION

VariantBam is a tool to extract/count specific sets of sequencing reads from next-generational sequencing files.

::DEVELOPER

VariantBam team

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 VariantBam

:: MORE INFORMATION

Citation:

VariantBam: filtering and profiling of next-generational sequencing data using region-specific rules.
Wala J, Zhang CZ, Meyerson M, Beroukhim R.
Bioinformatics. 2016 Feb 26. pii: btw111.

gffcompare 0.9.6f – Comparing, Annotating, Merging and Tracking Transcripts in GFF files

gffcompare 0.9.6f

:: DESCRIPTION

gffcompare is a program for comparing, annotating, merging and tracking transcripts in GFF(General Feature Format) files

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffcompare

:: MORE INFORMATION

gffread 0.94f – Filtering, Converting and Manipulating GFF files

gffread 0.94f

:: DESCRIPTION

The program gffread can be used to validate, filter, convert and perform various other operations on GFF (General Feature Format) files.

::DEVELOPER

The Center for Computational Biology at Johns Hopkins University

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Mac OsX

:: DOWNLOAD

 gffread

:: MORE INFORMATION

SBFC 1.3.7 – Systems Biology Format Converter

SBFC 1.3.7

:: DESCRIPTION

SBFC aims is to provide a generic framework that potentially allows any conversion between two formats. Interoperability between formats is a recurring issue in Systems Biolog

SBFC Online Version

::DEVELOPER

Computational Systems Neurobiology Group – Systems Biology of Neuronal Signalling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows
  • JRE

:: DOWNLOAD

 SBFC

:: MORE INFORMATION

Citation

The systems biology format converter.
Rodriguez N, Pettit JB, Dalle Pezze P, Li L, Henry A, van Iersel MP, Jalowicki G, Kutmon M, Natarajan KN, Tolnay D, Stefan MI, Evelo CT, Le Novère N.
BMC Bioinformatics. 2016 Apr 5;17(1):154. doi: 10.1186/s12859-016-1000-2.

PDB2PQR 2.1.1 – Convert Protein files in PDB format to PQR format

PDB2PQR 2.1.1

:: DESCRIPTION

PDB2PQR is a Python software package that automates many of the common tasks of preparing structures for continuum electrostatics calculations, providing a platform-independent utility for converting protein files in PDB format to PQR format.

::DEVELOPER

PDB2PQR Team

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • Python

:: DOWNLOAD

PDB2PQR

:: MORE INFORMATION

Citation

Dolinsky TJ, Czodrowski P, Li H, Nielsen JE, Jensen JH, Klebe G, Baker NA.
PDB2PQR: Expanding and upgrading automated preparation of biomolecular structures for molecular simulations.
Nucleic Acids Res, 35, W522-5, 2007.

VCF-Miner 4.0.1 – Analysis of VCF files

VCF-Miner 4.0.1

:: DESCRIPTION

VCF-Miner is a graphical user interface for sorting, filtering and querying information encoded in VCF (Variant Call Format) files.

::DEVELOPER

Bioinformatics Program, Division of Biomedical Statistics and Informatics, Mayo Clinic Research

:: SCREENSHOTS

VCF-Miner

:: REQUIREMENTS

  • Linux / Windows

:: DOWNLOAD

 VCF-Miner

:: MORE INFORMATION

Citation

VCF-Miner: GUI-based application for mining variants and annotations stored in VCF files.
Hart SN, Duffy P, Quest DJ, Hossain A, Meiners MA, Kocher JP.
Brief Bioinform. 2016 Mar;17(2):346-51. doi: 10.1093/bib/bbv051.

PedCut 1.19 – Cutting large and complex Pedigrees for Linkage Analysis

PedCut 1.19

:: DESCRIPTION

PedCut is a program for cutting complex pedigree into computable sub-pedigrees with user-specified MaxBit size

::DEVELOPER

Group of the Methods of Genetic Analysis

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux
  • Perl

:: DOWNLOAD

 PedCut

:: MORE INFORMATION

Citation:

Eur J Hum Genet. 2008 Jul;16(7):854-60. doi: 10.1038/ejhg.2008.24. Epub 2008 Feb 27.
An approach for cutting large and complex pedigrees for linkage analysis.
Liu F, Kirichenko A, Axenovich TI, van Duijn CM, Aulchenko YS.

CoGI – Towards Compressing Genomes as an Image

CoGI

:: DESCRIPTION

CoGI is a novel approach for genome compression, which transforms the genomic sequences to a two-dimensional binary image (or bitmap), then applies a rectangular partition coding algorithm to compress the binary image.

::DEVELOPER

The ADMIS group

:: SCREENSHOTS

N/A

::REQUIREMENTS

  • Linux

:: DOWNLOAD

 CoGI

:: MORE INFORMATION

Citation

IEEE/ACM Trans Comput Biol Bioinform. 2015 Nov-Dec;12(6):1275-85. doi: 10.1109/TCBB.2015.2430331.
CoGI: Towards Compressing Genomes as an Image.
Xie X, Zhou S, Guan J.