18th March 2016
ODIN-0.4.1 is released to overcome issues with the version of numpy (1.10.4), scipy (0.17.0), sklearn (0.17.1) and pysam (0.9.0). Moreover, ODIN is now available under the GPL v3 licence. ODIN-0.4.1 automatically copies the wigToBigWig tool into the PATH. We provide also some bug fixes:
- change the foldchange to define a differential peak
- filter differential peaks when option –no-correction is used
8th July 2015
ODIN-0.4 provides some improvements:
- improvement of the read size estimation,
- input validation, if chromosome size file, genome file and BAM files contain the same chromosome names,
- ODIN keeps lists of differential peaks (BED and narrowPeak) with non-corrected p-values (files have -uncor in name),
- improvement of the description of the –region parameter: whole analysis is done on the given regions; this includes in particular the HMM estimation,
- small bugfix if ‘chr’ is missing in BAM files
Moreover, we are happy to announce THOR, an extension of ODIN dealing with technical and biological replicates.
25th February 2015
ODIN-0.3.2 can now be run on Mac OS. Furthermore, we have fixed a small bug that occurs when analysing data where the corresponding input-DNA does not overlap. We have not added any further functionality to ODIN-0.3.2.
19th February 2015
We get rid of ODIN’s requirement to have a particular version of scikit installed. The maintainer of scikit swapped out their HMM implementation to the hmmlearn package. ODIN-0.3.1 has no additional functionality, but uses the HMM of hmmlearn instead of scikit.
29th January 2015
ODIN-0.3 now performs a Benjamini/Hochberg p-value correction. You can use the option –no-correction to switch it off. We therefore increased the default p-value cutoff from 0.05 to 0.1. You can change this cutoff with the option -p.
You can now determine the working directory with the option –output-dir. All files generated by ODIN a stored in the desired folder.
We fixed a bug that appears in the fragment size calculation when using a BAM files where no DNA sequence is stored. Moreover, the option –bibtex gives the BibTeX entry of our paper.
4th December 2014
With ODIN-0.2, I have fixed several bugs and implemented new features:
- bugfix: merge differential peaks and filter p-value by predefined threshold
- bugfix: peaks were shifted by 25bp
- additionally output differential peaks in narrowPeak format
- add more optional parameters with more informative descriptions, emphasize the ‘-m’ parameter for histone data
- write more infos to *-setup.info
- use other name for output signal: <experiment’s name>-<BAM filename>-normalized.bw
Furthermore, I have updated the website with information where ODIN’s parameters are described in our paper.
I have also created a googleGroup for ODIN.
17th November 2014
ODIN-0.1.1 release with bugfix for BigWig construction, ODIN gives now a warning if wigToBigWig is not found in $PATH
2nd October 2014