DESeq2 1.36.0 – Differential Expression Analysis for Sequence Count Data

DESeq2 1.36.0

:: DESCRIPTION

DESeq is an R package to analyse count data from high-throughput sequencing assays such as RNA-Seq and test for differential expression.

::DEVELOPER

Huber Group

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux/ Windows/MacOsX
  • R package
  • Bioconductor

:: DOWNLOAD

 DESeq

:: MORE INFORMATION

Citation

Genome Biol. 2014;15(12):550.
Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2.
Love MI, Huber W, Anders S.

Genome Biol. 2010;11(10):R106. doi: 10.1186/gb-2010-11-10-r106. Epub 2010 Oct 27.
Differential expression analysis for sequence count data.
Anders S, Huber W.

tweeDEseq 1.30.0 – Analyzing RNAseq Count data

tweeDEseq 1.30.0

:: DESCRIPTION

tweeDEseq is an R package for analyzing RNAseq count data. It implements Poisson-Tweedie family of distributions to model count data distribution. This family includes Poisson and Negative Bionomial as particular cases. The testPT test is used to detect genes that are differentially expressed (DE).

::DEVELOPER

Bioinformatic Research Group in Epidemiology

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / Windows/ MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 tweeDEseq

:: MORE INFORMATION

Citation

BMC Bioinformatics. 2013 Aug 21;14:254. doi: 10.1186/1471-2105-14-254.
A flexible count data model to fit the wide diversity of expression profiles arising from extensively replicated RNA-seq experiments.
Esnaola M1, Puig P, Gonzalez D, Castelo R, Gonzalez JR.

TCC 1.10.0 – Differential Expression Analysis for Tag Count data with Robust Normalization Strategies

TCC 1.10.0

:: DESCRIPTION

TCC provides a series of functions for performing differential expression analysis from RNA-seq count data using robust normalization strategy (called DEGES).

::DEVELOPER

Jianqiang Sun <wukong at bi.a.u-tokyo.ac.jp>, Tomoaki Nishiyama <tomoakin at staff.kanazawa-u.ac.jp>, Koji Kadota

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows/Linux/MacOsX
  • R
  • BioConductor

:: DOWNLOAD

 TCC

:: MORE INFORMATION

Citation

TCC: an R package for comparing tag count data with robust normalization strategies.
Sun J, Nishiyama T, Shimizu K, Kadota K.
BMC Bioinformatics. 2013 Jul 9;14:219. doi: 10.1186/1471-2105-14-219.

OpenCFU 3.9.0 – Software tool to Count Cell Colonies Growing on Plates

OpenCFU 3.9.0

:: DESCRIPTION

OpenCFU is a free software that should facilitate (and render more reproducible) the enumeration of colony forming unit (CFU).

::DEVELOPER

Quentin Geissmann

:: SCREENSHOTS

OpenCFU

:: REQUIREMENTS

  • Linux/ Windows

:: DOWNLOAD

 OpenCFU

:: MORE INFORMATION

Citation

PLoS One. 2013;8(2):e54072. doi: 10.1371/journal.pone.0054072. Epub 2013 Feb 15.
OpenCFU, a new free and open-source software to count cell colonies and other circular objects.
Geissmann Q.

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

Cell Counter 3.3 – Count Cells

Cell Counter 3.3

:: DESCRIPTION

Cell Counter is for counting cells (or other things). There is a choice for 4, 8, 12, 16 counters. Different (default) alarms and names. There is also a total sum with alarm. Custom settings, copy to Excel, etc..

::DEVELOPER

AMC, CMO, Amsterdam, The Netherlands – Contact: R.A.Hoebe -at- amc.nl

:: SCREENSHOTS

:: REQUIREMENTS

  • Windows

:: DOWNLOAD

Cell Counter

:: MORE INFORMATION

This software is free to anyone, just for fun send author a postcard:
AMC, Cell biology & Histology CMO, Ron Hoebe, Room M3-106-1
Meibergdreef 15, 1105 AZ  Amsterdam, The Netherlands

Count 10.04 – Evolutionary Analysis of Phylogenetic Profiles and Other Numerical Characters

Count 10.04

:: DESCRIPTION

Count is a software package for the evolutionary analysis of homolog family sizes (phylogenetic profiles), or other numerical census-type characters along a phylogeny. The principal data consist of the distribution of homolog family sizes across multiple genomes: for each (gene) family, that table gives the number of homologs identified in each genome.

::DEVELOPER

Miklós Csűrös.

:: SCREENSHOTS

Count

:: REQUIREMENTS

  • MacOsX / Linux /Windows
  • Java

:: DOWNLOAD

  Count

:: MORE INFORMATION

Citation

Bioinformatics. 2010 Aug 1;26(15):1910-2. doi: 10.1093/bioinformatics/btq315. Epub 2010 Jun 15.
Count: evolutionary analysis of phylogenetic profiles with parsimony and likelihood.
Csurös M.

Plasmodium Autocount 0.1 – Count Red Blood Cells infected with Plasmodium

Plasmodium Autocount 0.1

:: DESCRIPTION

Plasmodium Autocount automatically identify red blood cells and red blood cells infected with Plasmodium in a set of images. The software identifies cells using a circlular Hough transform, then looks for stained spots within cells as evidence of infection. Identified cells that are misshapen (debris on the slide) or have too much stain (white blood cells) are discarded.

::DEVELOPER

Victorian Bioinformatics Consortium

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows
  • Python

:: DOWNLOAD

 Plasmodium Autocount

:: MORE INFORMATION

Citation

Malar J. 2010 Dec 1;9:348. doi: 10.1186/1475-2875-9-348.
Automated estimation of parasitaemia of Plasmodium yoelii-infected mice by digital image analysis of Giemsa-stained thin blood smears.
Ma C, Harrison P, Wang L, Coppel RL.

Breakpoint Calculator 0.2.1 – Calculate Breakpoint Counts for each pair and triplet of Genomes

Breakpoint Calculator 0.2.1

:: DESCRIPTION

Breakpoint Calculator calculates pairwise and three-way hidden breakpoint counts for each pair and triplet of genomes.The breakpoint calculator constructs a weighted graph from the adjacencies of the genomes in the alignment and computes a maximum weight perfect matching.

::DEVELOPER

Birte Kehr., Knut Reinert, and Aaron Darling

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Linux / MacOsX / Windows

:: DOWNLOAD

  Breakpoint Calculator

:: MORE INFORMATION

Citation

Birte Kehr, Knut Reinert, Aaron Darling
Hidden breakpoints in genome alignments
WABI 2012

OligoCounter 0.64 – Count Overrepresented 8-14bp Oligonucleotides in DNA Sequences

OligoCounter 0.64

:: DESCRIPTION

OligoCounter is a Java command line program which counts overrepresented 8-14bp oligonucleotides in DNA sequences. These oligos can be useful in visualising small genomes on a global basis (see figure below), investigating repeats at certain regions, and for attributing short reads (for example from metagenomics) to a sequenced genome.

OligoViz : allows direct visualisation of OligoCounter data

OligoWords : generates 4mer data for JCircleGraph (use the perl script to extract 4mer data from a fasta file).

JCircleGraph : visualisation of 4mer and OligoCounter data in attractive genome atlases (requires 4mer files from OligoWords!).

::DEVELOPER

Dr Colin F. Davenport

:: SCREENSHOTS

N/A

:: REQUIREMENTS

  • Windows / Linux / MacOsX
  • Java

:: DOWNLOAD

 OligoCounter

:: MORE INFORMATION

Citation

Davenport, C. F., Wiehlmann, L., Reva, O. N. & Tümmler, B.
Visualization of Pseudomonas genomic structure by abundant 8-14mer oligonucleotides.
Environ Microbiol. 2009 May;11(5):1092-104.