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SeqMonk Changelog

What's new in SeqMonk 0.32.0

Aug 19, 2015
  • Added a duplication plot which provides an easier way to get as assessment of the level of technical (as opposed to biological) duplication in your data. The idea for the basic structure of the plot was taken from dupRadar (http://sourceforge.net/projects/dupradar/) which is a bioconductor package which allows this type of plot to be created in a more automated fashion.
  • Added a binomial for/rev statistical test which is useful for comparing bisulphite datasets where there is an overall change in the level of methylation between your samples, and you want to know which points change to an unusual level rather than just finding ones which change at all.
  • Changed the auto create groups/set tool to operate sequentially so a data set won't be added to more than one group.
  • Fixed a bug where gff3 files in custom genomes weren't being loaded.
  • Fixed a bug where you couldn't edit preferences if your R executable was found in the path.
  • Added a data export option to the quantitation trend plot.
  • Added a check to the windows launcher for people trying to run SeqMonk on a 64 bit windows system, but using only a 32 bit version of the JRE.

New in SeqMonk 0.31.1 (Jul 14, 2015)

  • Changed paired end SAM/BAM import to not rely on the TLEN SAM field
  • Fixed a bug in logistic regression when only analysing probes on a single chromosome
  • Updated the MA plot to the same feature set as the scatterplot
  • Added version checking to R installation validation

New in SeqMonk 0.31.0 (Jul 14, 2015)

  • Added DNA contamination estimation and paired end support to the RNA-Seq pipeline
  • Added an import filter for methylkit data
  • Added an option to save the underying data in QC plots
  • Added an option to extract the centres of reads to the visible stores parser
  • Added a for/rev binomial statistics test
  • Improved the UI when long names are used for data stores or probe lists
  • Various bug fixes

New in SeqMonk 0.30.2 (May 18, 2015)

  • Worked around an Adobe Illustrator bug which was causing SeqMonk SVG files to not load cleanly
  • Added a work round for installing R dependencies for unprivileged users without a local R library
  • Added better up-front data validation for the DESeq2 and EdgeR filters

New in SeqMonk 0.30.1 (May 1, 2015)

  • A bug fix release which addresses an issue in the installation of R dependencies in the v0.30.0 release.

New in SeqMonk 0.30.0 (Apr 24, 2015)

  • A major release which adds some significant new statistical capabilities to the program.
  • The major function in this release is the addition of a bridge between seqmonk
  • and R which allows seqmonk filters to use R scripts to do the statistical
  • calculation, but then transparently import the results back into SeqMonk. This
  • requires a new set of preferences to locate R and to manage the dependencies
  • used within the filters.
  • Functionality added in this release is:
  • Added a DESeq2 based statistical filter for count based sequence data
  • Added an EdgeR based statistical filter for count based sequence data
  • Added a logistic regression filter for bisulphite sequence data with replicates
  • Added a gene set intensity difference filter for functional analysis
  • Added an import filter for Bismark coverage (.cov) files
  • Removed the option to import paired end data as HiC since this makes no sense
  • Changed the way you select data / control pairs in the relative quantitation to make it clearer
  • Fixed memory checking bug on systems with non EN_US language settings
  • Added a plot to graphically show the relationships between multiple probe lists
  • Make the RNA-Seq pipeline not create new probes if the probes it will make are just the same as the current set.
  • Added an import filter for QuasR data
  • Fix loading of help files when you have non ASCII characters in your path
  • Make the custom genome builder understand compressed fastq and gff files
  • Fix a memory bug introduced in Java8 for 32 bit JVMs
  • In addition a number of minor bugs have been fixed and some performance optimisations have been included.

New in SeqMonk 0.29.0 (Dec 17, 2014)

  • A major release which adds a set of new features which are likely to be of use in studies which contain large numbers of samples (for example single cell experiments) as well as other general improvements.
  • Added an Even Coverage probe generator to make probes with the same number of reads in them over the whole genome.
  • Added an exportable scale display to the data zoom control so you can add this to figures easily.
  • Added the ability to show variability in a number of different ways when showing replicate sets in the chromosome view.
  • Added the ability to split replicate sets into their component tracks in the chromosome view.
  • Added code to auto-detect the most likely import settings for paired end and spliced BAM files and to set these as the defaults.
  • Optimised the importing of spliced BAM files so they should now load significantly more quickly than before.
  • Put all of the chromosome display options into a single preferences pane and removed them from the toolbar, replacing them with a button to open the new pane.
  • Added an active transcription quantitation pipeline which quantitates reads in introns rather than exons.
  • Added an option to the data store tree to re-order the tracks in the display based on their correlation.
  • Added options to the read position probe generator. It can now operate within just the currently visible region, and can group valid positions together in sets.
  • Removed the option to have empty probes discarded during probe generation since there are better ways to do this now.
  • Improved the display of data tracks so that we can stack more of them into a standard view.

New in SeqMonk 0.28.0 (Oct 24, 2014)

  • Added more options to the Distance to Feature quantitation
  • Improved the efficiency with which large HiC heatmaps are drawn
  • Added a tabular view to show the levels of overlaps between a set of probe lists
  • Added the Star Wars plot for plotting means and confidence intervals in a manner similar to a boxplot.
  • Added a genetrap quantitation pipeline
  • Added a proportion of library statistics filter
  • Added a euclidian distance mode for heirarcical clustering
  • Added an RNA-Seq QC plot
  • Added the ability to normalise in groups when doing Match Distributions
  • Added an option to go to a centred window of a specified size
  • Changed the quantitation model to allow probes in individual samples to not store a value. Applied this to Bisulphite Quantitation rather than using flag values to indicate probes which didn't have enough data to calculate a value. Changed the default filtering options to be much more lax.
  • Added a BAM import option to choose to import only primary alignments from a BAM file, and made this the default.
  • Added a popup menu item to make it easy to convert probe lists into annotation tracks
  • Added a small RNA QC plot
  • Added an import option for text files which contain a position and a count
  • Added an option to do bulk find/replace renaming of DataSets
  • Added a new Percentile Feature Probe Generator which makes sets of probes spaced evenly over features.
  • Fixed a bug in the MACS caller when there were very low numbers of reads.
  • Added a display option to show data as coloured blocks rather than bars.
  • Added the option to reverse any selected gradient in the chromosome view.
  • Added an option to design running window probes only within the currently visible region.

New in SeqMonk 0.27.0 (Oct 24, 2014)

  • New features include:
  • Improved the RNA-Seq quantitation to not group together features with the same name which don't physically overlap.
  • Added an option to the visible stores parser to filter reads by length during import.
  • Added an option to the visible stores parser to down-sample large datasets.
  • Added a new tool to automatically create sample groups or replicate sets based on finding text patterns within the sample names.
  • Bugs fixed include:
  • GFF3 files are now added to new custom genomes by default
  • Improved the efficiency of removing large numbers of tracks from the view
  • Increased the default stack size to fix a bug in sorting very large numbers of reads.
  • Made efficiency improvement in the loading of HiC datasets.
  • Removed debugging code from the HiC heatmap view which was causing slow downs
  • Fixed a bug in p-value multiple testing correction in HiC heatmaps which could create negative p-values when large numbers of comparisons were made.

New in SeqMonk 0.26.0 (Oct 29, 2013)

  • Fixed the launcher on OSX to adapt to changes in OSX Mavericks which broke the auto configuration code.
  • Fixed a bug which caused the program to hang after downloading a new genome in response to opening an existing seqmonk project.
  • Added a new graphical tool to aid in the creation of custom genomes meaning that you can now create custom genomes including pseudo chromosomes from either a collection of fasta files or a GTF file.

New in SeqMonk 0.24.1 (May 9, 2013)

  • The quantitated values calculated by the RNA-Seq pipeline were incorrect if you chose not to merge transcript isoforms when performing the quantitation.The total count correction was incorrectly being performed on the total number of bases in the
  • data instead of the total number of reads.This meant that the values reported were much lower than they should have been. However, the values would all have been lower by the same factor so any differential analysis performed would still be valid.If
  • you repeat the analysis with the fixed verison you should get the same result, but with absolute values which are much higher.
  • The visible stores parser was broken and produced an error instead of re-importing data.This is now fixed.
  • The MACS probe generator was using the default values for all analyses and wasn't picking up changes made by the user. This is now fixed.
  • The MACS probe generator wasn't correctly resetting after a cancelled run and had to be completely restarted to work again. This is now fixed.
  • The intensity difference filter would throw an error if it was run with a probe list containing fewer than 100 probes.This is now fixed, and the filter will also now issue a warning if you try to use an already filtered list to run it.
  • An improvement has been made to the random coverage estimation for the MACS parser which takes the read lengths rather than just their number into account.
  • A formatting bug which affected the axes of the probe trend plot has been fixed.This caused very large decimal numbers to be shown in the y axis and often these were positioned all on top of each other in the middle of the axis.This should now be resolved.
  • There was a bug which allowed no lists to be selected in the highlight sublists option of the scatterplot. This is now fixed.

New in SeqMonk 0.24.0 (Feb 12, 2013)

  • Added the ability to export all probe reports in GFF format
  • Added a pipeline to detect antisense transcription from directional RNA-Seq libraries.
  • Added a system which can provide immediate feedback to submitted crash reports if they're ones we've seen before and for which we can offer useful feedback.
  • Added a chi-square based contingency test filter which is useful for bisulphite sequencing libraries (and possibly others too).
  • Added an ID field to reports for cases where the name of a feature isn't useful or unique
  • Added a probe length quantitation option
  • Added a probe name filter which allows you to specify a large list of names and selects probes which match any of them
  • Added an option to merge all transcripts in the RNA-Seq pipeline to create a single gene level measure of transcription
  • Changed the active store parser to a visible stores parse to allow the easy re-import of multiple datasets in a single operation
  • Added an option to generate raw counts to the RNA-Seq quantitation pipeline to allow for easy interfacing with tools such as DESeq which require this
  • Added a smoothing subtraction quantitation method which can be used to
  • detect sudden local changes in quantitation
  • Added the ability to select the order of highlighted probe lists in the scatterplot
  • Some changes have also been made to address problems in previous versions:
  • We fixed a bug which would produce incorrect p-values following multiple
  • testing correction, but only affected p-values which were initially very
  • high (p>~0.3)
  • We fixed an unnecessary level of multiple testing correction in the intensity difference filter which meant that some candidates which could have been reported were not.Typically we see around a 10% increase in the number of candidates in the new correction method over the previous version.
  • We changed the behaviour of the BAM import filter for paired end data which were mapped with a spliced read mapper.We now show the second read of the pair with the same direction as the first read to indicate the direction of the fragment and preserve the direction in strand specific libraries.
  • The "load probes from file" probe generator has been removed. It was never very well supported and its functionality is better performed by importing the data into an annotation track and using the feature probe generator.
  • A couple of timing bugs were fixed which prevented the import of extra annotation on some linux installations.
  • In HiC analysis we have removed some optimizations in the testing which were leading to unrealistically low p-values for some interactions. We now test against the full set of possible interactions, only making an exception to correct for only cis interactions when all trans interactions have been specifically excluded.

New in SeqMonk 0.21.0 (Jun 4, 2012)

  • Added full tracking to all filters
  • Added Monte-Carlo statistics filter
  • Added bisulphite quantitation pipeline
  • Added Hierarchical clustering tool
  • Added HiC cis/trans quantitation method
  • Made Scatter/MA plots interactive
  • Added option to make multiple 4C datasets easily
  • Improved HiC heatmaps and associated tools
  • Fixed bug in HiC import for data with warnings
  • Fixed SVG corruption bug
  • Fixed Boxwhisker scaling display bug

New in SeqMonk 0.19.0 (Jan 6, 2012)

  • Greatly improved load and save speed
  • Greatly reduced memory profile
  • Higher read densities in the chromosome view
  • More colour options in the chromsome view
  • Improved aligned probes plot

New in SeqMonk 0.18.0 (Dec 4, 2011)

  • Added RNA-Seq Quantitation pipeline
  • Improved loading speed on multi-CPU machines
  • Added HiC probe matrix view
  • Improved controls for HiC plots
  • Added SeqMonk reimport parser to pass data between projects
  • Fixed MA Plot label positions
  • Fixed distance filtering in HiC plots
  • Fixed windows launcher for non-english locales
  • Fixed generic text import on gzipped files

New in SeqMonk 0.17.1 (Sep 28, 2011)

  • Fixed a launcher bug for OSX systems with more than 10GB RAM
  • Fixed a bug when creating HiC heatmaps with more than 44k probes
  • Added an option to send HiC coordinates back to the chromosome view
  • Added a fixed value quantitation method

New in SeqMonk 0.17.0 (Sep 25, 2011)

  • Added support for HiC read data
  • Added a native windows exe launcher
  • Launchers now auto-configure memory settings
  • Added support for very large annotation sets
  • Added a Z-score transformation option to the quantitation tools
  • Added a match distribution option to the quantitation tools
  • Added a new statistical filter for pairwise comparison of samples without replicates
  • Added an MA plot view
  • Allow data import to be cancelled
  • Allow annotation import for multiple files in a single operation
  • Added support for gzipped files in all data import filters
  • Added a preview panel when browsing for projects to open
  • Changed (again!) the way log transformed empty probes are handled

New in SeqMonk 0.16.0 (Jul 6, 2011)

  • Added a launch script for linux so you don't have to write out your own launch command
  • Added a work round to allow importing paired end tophat files
  • Added an option to save feature search results as an annotation track
  • Manual correlation filter can now correlate against up to 12 profiles simulataneously
  • Percentile normalisation quantitation can use a probe list to calculate the normalisation factor
  • The probe trend plot can now operate over the currently visible region of the chromsome view

New in SeqMonk 0.15.0 (May 25, 2011)

  • Allow import of introns from spliced BAM/SAM files
  • New probe generator to make probes over every different read position
  • New probe generator to merge and deduplicate an existing probe set
  • New quantitation method to count exact overlaps between reads and probes
  • Feature import from GFFv3 and GTF files
  • Changed the way empty probes are handled during quantitation
  • Allow zooming within histograms
  • New trend plot options to weight all probes equally in the final plot

New in SeqMonk 0.14.1 (Apr 12, 2011)

  • Fixed an import bug for paired end data in BAM/SAM format. If you use these please read the release notes
  • Fixed a minor import bug in paired end bowtie files
  • Improved the smoothing of trend plots
  • Added an option to put running window probes inside an existing probe set
  • Added an option to reverse all reads in a data set

New in SeqMonk 0.14.0 (Feb 9, 2011)

  • Added a cumulative distribution plot
  • Added a percentile normalisation quantitation method
  • Added a scale to the genome view
  • Allow the import of multiple annotation files in the same operation
  • Fixed a load of bugs (see release notes)

New in SeqMonk 0.13.1 (Jan 14, 2011)

  • Added a correlation matrix display
  • Added proper scales to all figures and graphs
  • Fixed a number of important bugs (see release notes)

New in SeqMonk 0.13.0 (Dec 1, 2010)

  • Data can now be imported from BAM files
  • Quantitations can be exported in BedGraph format
  • New line graph display for examining trends over multiple data stores
  • New clustering and correlation tools for identifying groups with similar quantitation profiles
  • Added a per-probe normalisation quantitation method

New in SeqMonk 0.12.0 (Oct 2, 2010)

  • Added a whole genome quantitated data view
  • Fixed a genome update bug when only a single track was in the chromosome view
  • Fixed a crash in the Replicate Set editor

New in SeqMonk 0.11.0 (Sep 14, 2010)

  • Fixed importing SAM files containing unmapped reads
  • Can now import bismark files which split up CHH and CHG methylation context
  • Biological replicates can now be grouped into replicate sets
  • Added a statistical filter for biological replicates
  • Added an aligned probe view to look at individual probe trends
  • Allow plotting of multiple probe lists in a boxwhisker plot

New in SeqMonk 0.10.1 (Jul 2, 2010)

  • Fixed a bug which removed drawing optimisation in the chromsome viewer
  • Fixed a bug which caused the genome viewer to list negative positions
  • Enabled some new layout options for packed read data