Here is a list of all software I have designed over the years. Feel free to use them in your research. For a more up-to-date list of Software, please visit my GitHub account.
tailfindr is a R package for estimating poly(A)-tail lengths in Oxford Nanopore reads. It can work on both RNA and cDNA reads. For cDNA reads, in addition to estimating poly(A) tail length, it can also estimate poly(T) tail lengths in the complementary reads.
tailfindr can work on reads that have been basecalled with either standard or flipflop basecalling models.
Analyze4d is a comprehensive tool for region-of-interest/time course analysis of functional magnetic resonance imaging (fMRI) data. This MATLAB-based tool is open source and is completely GUI based, so no experience of any programming language, whatsoever, is needed to use it.
Analyze4D has a number of tools to help you select regions of interest and analyze the time-series of voxels inside these regions of interest. Coupled with its ability to read common neuroimaging data formats, Analyze4D enables anyone involved with fMRI to use this tool for analyzing their data at any stage in their analysis.
Zoom & pan
Overlay activation maps
Plot motion regressors
Plot voxel time courses
Plot subtraction images
Overlay ROIs from AAL atlas
Completely GUI driven
Donders real-time fMRI pipeline
Based on just single language, the pipeline is very flexible and easy to use. Whether it's experiment control, decoding, or dynamic stimulus generation, everything can be designed in our pipeline using MATLAB tools that we have specifically developed for each of these tasks.
Old versions of this pipeline are already included in FieldTrip distribution. The new vastly improved pipeline is however currently under active development. We will soon release a stable version of this pipeline.
Multilanguage Implicit Association Test (IAT) for measuring aggression
This is a computer based Implicit Association Test for measuring aggression. The IAT is designed in Millisecond Inquisit software so you will need to install Inquisit on the PC you want to run this IAT on. This particular IAT can be conducted in three different languages: German, Dutch, and English. The IAT is immediately followed by a demographic questionnaire.
Inquisit standardized our IAT making it easier for everyone to use. You can download this revised version of our IAT below:
Download revised IAT from Inquisit
If you want to find more information about this IAT, please read the following paper:
Effect of music tempo in First-Person Shooter on arousal and aggression
Feel free to drop me a line if you have any problem using this IAT.
Vividness of mental imagery questionnaire (VVIQ)
This is a computer-based vividness of mental imagery questionnaire (VVIQ) [1, 2, 3] designed in Millisecond Inquisit software. The VVIQ is immediately followed by a demographic questionnaire.
1. David F. Marks. Visual imagery differences in the recall of pictures. British journal of psychology London England 1973, 64(1):17–24, 1973
2. VVIQ by David F. Marks. City University London
3. Paul J. Chara, Jr. and William S. Verplanck. The Imagery Questionnaire: An Investigation of its Validity