Software Listing of Author : "Babraham Bioinformatics"

ChIPMonk is a powerful application designed to provide visualisation and analysis of ChIP-on-chip data. ChIPMonk is a program to enable the visualisation and analysis of ChIP-on-chip data. It's main features are: Import of data from Nimblegen arrays (other formats can be added if people send us examples!) Noramlisation of data (both per array and per probe) Various data plotting options to assess data quality and the effectiveness of normalisation Creation of data groups for visualisation and analysis Visualisation of data against an annotated genome. Statistical analysis of data to find probes of interest Creation of reports containing probes, data and genome annotation

  • Platform: WinOther

Difference tracker is a graphic plugin designed to track a large collection of faint objects. Difference tracker was originally developed to analyse the movement of mitochondria through axons.

This type of data features a large number of moving particles which often exhibit low contrast against the background and can move behind stationary objects. The aim for this kind of data was not to get the most complete track possible for any individual particle, but to collect relevant aggregate statistics for the movie as a whole.

Difference tracker contains of two ImageJ plugins. Difference filter extracts the moving parts of an image to enhance the contrast of the motile particles. From there the Mass Particle Tracker tracks this large set of particles and works out a set of statistics for the number, size and rate...

  • Platform: WinOther
  • FastQC
  • License: Shareware
  • Price:

FastQC is a powerful application designed to provide a simple way to do quality control checks on raw sequence data coming from high throughput sequencing pipelines. It provides a modular set of analyses which you can use to give a quick impression of whether your data has any problems of which you should be aware before doing any further analysis for WindowsAll

  • Platform: WinOther

FocalPoint is a handy image viewer designed to offer a few significant enhancements over the file browser which comes with your operating system.

As well as working with normal single frame images (png, jpeg etc) it also has support for multi-frame image stacks (tiff, avi), and specialised formats used by various microscope manufacturers (lsm, oif, oib). For multi frame and multi channel images it allows you to change between frames and channels at will.

Focalpoint also has a very flexible system whereby you can interactively change the size of the thumbnails you are shown to allow you to see the level of detail you require for WindowsAll

  • Platform: WinOther

FRET Saw is a handy application created to enable you to to view pairs of images from FRET experiments.

In addition to displaying the two FRET channel images side by side the program also calculates a FRET image which is colourised by the ratio of the intensities in the two source images. There are various options for subtracting background and setting ratio ranges as well as the option to save the final combined image.

FRET Saw can take in 8 or 16 bit greyscale images either as TIFFs or as a properly ordered Olympus OIB file. for WindowsAll

  • Platform: WinOther

MZData Mass Spectrum Viewer is a little app designed to enable you to view mzData mass spec files. It is not designed to be a full analysis application, but rather to provide a quick view of mzData files. for WindowsAll

  • Platform: WinOther

Realyser is a little app designed to assist users in the normalization of QPCR data. for WindowsAll

  • Platform: WinOther

SeqMonk is a powerful application designed to enable you to visualize and analyze mapped sequence data.

It was written for use with mapped next generation sequence data but can in theory be used for any dataset which can be expressed as a series of genomic positions.

Features:

TE Import of mapped data from text files
TE Creation of data groups for visualisation and analysis
TE Visualisation of mapped regions against an annotated genome.
TE Flexible quantitation of the mapped data to allow comparisons between data sets
TE Statistical analysis of data to find regions of interest
TE Creation of reports containing data and genome annotation


  • Platform: Win7 x64, Windows 7, WinOther, WinVista, WinVista x64

SparkSpotter is a graphic plugin designed to identify short, bright spark events in movies and videos. It was originally designed to work with microsopy images of cell stained with flourescent dyes, but can probably be applied to many different types of input.

SparkSpotter works on 8 or 16 bit greyscale image stacks (movies). It can analyse either single or multiple pixels stacks looking for frames which show a sudden increase in intensity. It has the ability to smooth out any longer term changes in the overall brightness of the images.

The program features an interactive viewer to allow you to review the events SparkSpotter has found. You can also export the list of events from the viewer. for WindowsAll

  • Platform: WinOther

StackMeasure is a graphic plugin designed to enable you to identify features of interest and to allow you to measure the distance between them.

Interesting features are groups of spatially clustered voxels with the same (or similar) colour. StackMeasure can work with either with a single RGB image file, with separate black and white TIFF files (one for each channel), or with Zeiss lsm files. With RGB files you can set how much flexibility you want to allow in colour matching but with the other formats the channels are completely separated.

StackMeasure with then identify a set of features and give you details of their position and volume. It will generate a composite image stack, and can render a 3D version of your stack so you can better visualise the features.

Once you have defined your features...

  • Platform: WinOther
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