What's new in SeqMonk 1.47.0
Mar 22, 2022
- There are two major changes of note:
- The way the OSX package is built has been changed so that we can
- deal with the new security model in OSX v10.15 (Catalina). People
- working on that version will have found that they were unable to
- load or save data to anywhere other than their home directory.
- This new version now tests for limited disk access on OSX and if
- it finds it it will point to instructions for how SeqMonk can be
- given more generous permissions to read data from places like USB
- drives, network shares and the Desktop.
- We've made a relatively minor change to the way that RNA-Seq
- quantitation works. When we merge transcript isoforms we used to
- prefer matching transcripts based on them having compatible names
- (eg ABC-201 would merge with ABC-202), *and* based on them actually
- overlapping in the genome. We found though that some gene models
- from Ensembl broke these assumptions (ie there are cases with
- two different genes with identical names which overlap, and cases
- of genes with multiple transcripts which don't overlap). These
- cases are all nuts but they exist so we need to deal with them. We've
- now changed to prefer using the "gene_id" annotation on transcripts
- to decide which ones to merge, which deals better with these edge
- cases. What this means though is that if you have an existing
- RNA-Seq analysis in a project and you re-quantitate it having moved
- to the new SeqMonk version that your probe set will be replaced as
- it won't match the exsting set because of these changes. You will
- therefore need to either re-create your filtered lists using the
- new probe set - or stick to an older version of SeqMonk to finish
- off those existing projects.
- Other more minor changes are:
- Improve the default matching options and save name for annotated
- probe reports.
- Added a vistory event for adding annotation
- Added replicate set colouring to boxplots and beanplots
- Made the default heatmap colours more friendly to colourblind people
- Changed the min R version to 3.6 as Bioconductor is broken for
- versions older than that.
- Fixed a StarWars layout bug for multiple lists and one store.
- Use https to communicate with web services
- Try to improve R package installs on OSX
New in SeqMonk 1.42.0 (Jun 6, 2018)
- Fixed a data loss bug in import of sorted BAM files. Affects all sorted BAM files imported with v1.40.1 or v1.41.0. Read the release notes for details or see This bug report
- Added a size factor normalisation
- Added a quantitation heatmap plot
- Fixed problems with the linux theme in Ubuntu 18.04
- Worked round a problem with the installation of EdgeR on some systems
- Fixed a data update bug when creating custom genomes
New in SeqMonk 1.41.0 (Apr 4, 2018)
- Added a QQ plot
- Improved the logistic regression filter
- Fixed slowness when working with hundreds of data sets
- Added a way to update a project to a newer core annotation version
- Fixed the RNA-Seq QC plot when a rRNA track wasn't present
- Allowed multiple comparisons in the DESeq statistical filter
- Report the parameters estimated by the RNA-Seq pipeline
New in SeqMonk 1.40.1 (Feb 22, 2018)
- Changed the internal data model to store positions and counts separately to make the storage of heavily duplicated data much more efficient
- Added a LIMMA statistical filter
- Modified the GTF parser to better deal with the structure of Ensembl GTF files.
- Changed all of the launchers so you can pass a file name to open. Allows file extensions to be associated with seqmonk so you can open projects by double clicking on them.
- Improve the merging of transcripts in the RNA-Seq pipeline to use gene ids where they are present in the annotation so we don't get spurious merging of overlapping transcripts on the same strand which are annotated as belonging to different genes.
- Updated the genome processing scripts so that gene_ids are added to all transcripts
- Fixed a crash in the aligned probes plot when no data stores are visible
- Fixed a display bug for the list of features in the feature filter and quantitation trend plot.
- Fixed an inefficient packing algorithm when the number of reads was too great to be displayed within the available height of the chromosome view.
New in SeqMonk 1.40.0 (Jan 3, 2018)
- Restructured the statistical filteres
- Added an option to deal with duplication in RNA-Seq quantitation
- Added a new EdgeR filter for methylation data
- Added an option to change memory settings in the preferences
- Added an R debugging mode
- Added a strand bias plot
- Various bug fixes
New in SeqMonk 1.39.0 (Nov 6, 2017)
- Added the ability to support multiple annoation versions for the same genome assembly
- Added a BEDPE file format parser
- Added better absolute filtering for methylation data
- Added more statistics options for GeneSet statistics
- Improved the presentation and scaling of the aligned probes plot
- Fixed a crash in PCA
- Fixed a crash when exporting correlation matrices
- Fixed a bug when making replicate sets from the data store tree
New in SeqMonk 1.38.2 (Jul 18, 2017)
- Fixed a hang on OSX with the latest JRE when making reports
- Fixed a logic bug in setting perplexity defaults for Tsne
- Fixed a probe list duplication bug in the Gene Set Intensity Difference filter
- Improved the Gene Set Intensity Difference filter default values
New in SeqMonk 1.38.1 (Jun 9, 2017)
- Fixed a performance bug with large custom genomes
- Added a scale bar to the HiC heatmap
- Moved to using the Rtnse package for TSNE plotting
- Added extra launch script debugging
- Fixed a bug in the Splicing Efficiency pipeline
- Fixed a crash when labelling very similar samples in the PCA plot
New in SeqMonk 1.37.1 (Feb 7, 2017)
- Fixed:
- A crash reporter bug which makes it difficult to diagnose R based crashes
- A bug in custom genomes if feature names contained a forward slash
- Documentation updates
New in SeqMonk 0.34.1 (Jul 13, 2016)
- Fixed a crash in the beanplot when the first quantitated value was null
- Fixed a problem where small chromosomes couldn't be selected in the genome view
- Fixed a hang when trying to view very small probes in a report
New in SeqMonk 0.34.0 (Jul 13, 2016)
- Added a transcription termination quantitation pipeline to quantitate termination efficiency
- Added a front/back chi-square test to do stats analysis for the termination quantitation
- Added a beanplot display
- Added a default MAPQ filter of 20 when importing BAM files
- Allowed the read position generator to work inside an existing probeset
- Made the expanded replicate set display preference affect most plots which work on visible data stores
- Made the remote genomes list show the data of the annotation set used to create each genome
- Various smaller bug fixes and improvements
New in SeqMonk 0.33.0 (Jul 13, 2016)
- Added more metrics and allowed filtering in the RNA-Seq QC plot
- Allow the creation of multiple genome projects so we can accommodate control sets (ERCC for example)
- Improved the layout in the chromosome view when many data tracks are loaded
- Added a variance plot and a set of filters to select probes based on their variance
- Added a shuffled probe list probe generator
- Made the duplication plot work across multiple data stores
- Added probe names to the hierarcical cluster plot
- Fixed a bug when creating custom genomes from gff3 files
- Improved the data store tree so you can now create replicate sets based on the cluters seen
- Added a chromsome view report for bulk exporting chromosome view images
New in SeqMonk 0.32.1 (Sep 19, 2015)
- Fixed a bug which caused some systems to hang when running a monitored R script
- Improved the reporting of R crashes
- Fixed some layout issues where parts of the UI were not visible when using long Data Store names
- Made lines in the line graph plot selectable
New in SeqMonk 0.32.0 (Aug 18, 2015)
- Added a duplication plot based around DupRadar
- Added a binomial stats filter for bisulphite analysis where there is a global methylation change
- Fixed a bug in preferences editing for systems with R in the path
- Added a data export option to the quantitation trend plot
- Various bug and stability fixes
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 2, 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 12, 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)
- Fixed a bug in the installation of the DESeq2 R dependency
New in SeqMonk 0.30.0 (Apr 24, 2015)
- Added the ability for SeqMonk to link to R for some analyses
- Added a DESeq2 statistical filter
- Added an EdgeR statistical filter
- Added a logistic regression statitistcal filter
- Added a gene set intensity difference filter
- Added an import filter for Bismark cov files
- Added an import filter for QuasR files
New in SeqMonk 0.29.0 (Dec 16, 2014)
- Added and Even Coverage probe generator
- Added an exportable scale bar for the chromosome view
- Added a number of ways to show varaibility in replicate sets
- Added auto-dection of the most likely BAM import options
- Expanded and grouped the data track display options
- Added an active transcription quantitation pipeline
- Added the ability to re-order visible tracks based on the Data Store tree
- Added new options to the read position probe generator
- Improved the display of data tracks when large numbers of tracks are shown
New in SeqMonk 0.28.0 (Oct 24, 2014)
- Added the Star Wars plot
- Added RNA-Seq and Small RNA QC plots
- Removed flag values from the BS-Seq pipeline
- Added an option to import only primary alignments during BAM import
- Added an option to import text files which contain a position and a count
- Added an option to do bulk find-replace in dataset names
- Added a percentile feature probe generator
- Added a display option to show blocks instead of bars
- Added more options to the running window probe generator
- Added a proportion of library statistics filter
- Added more options to the distance to feature quantitation
New in SeqMonk 0.27.0 (Jan 11, 2014)
- Made improvements to the RNA-Seq and HiC Analysis tools
- Added a tool to automatically group DataSets based on their names
- Added options to downsample datasets or filter reads by their length
- Fixed a p-value correction bug in large HiC heatmaps
- Fixed a bug which occurred when sorting very large numbers of reads
- Fixed a bug when using GFFv3 files to create custom genomes
- Added warnings to pipelines which wipe out existing probe sets
New in SeqMonk 0.26.0 (Oct 25, 2013)
- Added a launcher fix to allow the program to work on OSX Mavericks
- Added a fix for a hang when loading a project using a genome not currently installed
- Added a graphical tool for creating custom genomes from fasta or GTF files
New in SeqMonk 0.25.0 (Sep 10, 2013)
- Added a quantitation trend plot to allow the examination of complex pattersn around features
- Added a muti-lane chi-square test for allele specific analysis and other applications
- Improved the options in the feature probe generator
- Allow multiple data stores in the aligned probes plot and allow custom sorting
- Allow filtering of reads against features when re-importing
- Added nice colour options to the hierarchical cluster plot
- Added a domainogram plot to look at quantitations at different levels
- Added an option to find sets of features using a list of search terms
- Added the ability to add comments to probe lists so you can remember why you did what you did
- Added a probe list description report to completely record the results of an analysis
- Added a subset normalisation quantitation method
- Reorganised the relative quantitation method to allow for specific pairings of references and samples
- Lots of other bug fixes and improvements
New in SeqMonk 0.24.1 (Feb 23, 2013)
- Fixed a bug in RNA quantitation for unmerged transcripts
- Fixed a bug causing MACS user options to not be read
- Fixed a crash in the visible store parser
- Fixed an axis label layout bug in the probe trend plot
- Fixed a crash in the intensity difference filter when run with a very small list of probes
New in SeqMonk 0.24.0 (Feb 12, 2013)
- Added GFF export option to reports
- Added antisense transcription pipeline
- Added automatic feedback to crash reports
- Added an ID field to reports
- Added a probe length quantitation
- Added a smoothing subtraction quantitation
- Added a probe name filter
- Added the ability to do gene level RNA-Seq quantitation
- Added a Chi-Square contingency test statistical filter
- Added a raw count option to the RNA-Seq pipeline
- Added the ability to specify the order of highlighted sublists in the scatterplot
New in SeqMonk 0.23.1 (Dec 11, 2012)
- Fixed a bug causing crashing from invalid chromosome names in imported data
- Allowed per-chromosome normalisation in the cis/trans quantitation
- Added per-chromsome filtering to the cis/trans scatterplot
- Added an option to export valid interaction ends into a probe list to the HiC heatmaps
New in SeqMonk 0.23.0 (Dec 3, 2012)
- Many improvements in existing HiC tools performance
- Improved HiC statistics
- Added a MACS style peak caller
- Added splicing efficiency quantitation pipeline
- Added name based probe filtering
- Windowed filters can now group by features
- Added sublist coloring to the scatterplot
- Added customizable color gradients to all gradient views
- Allow quantitations to be viewed as bars, lines or points
- Allow filtering by mapping quality when importing BAM/SAM
New in SeqMonk 0.22.0 (Sep 6, 2012)
- Major revision to all HiC tools - read the release notes!
- New HiC statistical model
- More controls on HiC heatmap creation
- Improved HiC import filters
- HiC cis:trans scatterplot
- Eigenvector quantitation method to detect chromatin domains
- New 4C enrichment quantitation method
- New consecutive probe generator
- Windowed filters can now use consecutive probes
- Added feature name filter
- Improved deduplication filter
New in SeqMonk 0.21.0 (Jun 5, 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 0.20.0 (Jun 5, 2012)
- Fixed a bug which corrupted filtered probe lists in probe sets containing multiple probes at exactly the same position - see release notes for details
- Fixed a bug which caused the Intensity Difference Filter to add the same hit multiple times
- Fixed a bug in the deduplicated view of HiC data
- Added a quantitation pipeline for wiggle type plots
New in SeqMonk 0.19.0 (Jun 5, 2012)
- Greatly improved load and save speed
- Greatly reduced memory profile
- Higher read densities in the chromosome view
- More color options in the chromsome view
- Improved aligned probes plot
New in SeqMonk 0.18.0 (Jun 5, 2012)
- 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 (Jun 5, 2012)
- 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 (Jun 5, 2012)
- 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 (Jun 5, 2012)
- 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 simultaneously
- Percentile normalization quantitation can use a probe list to calculate the normalization factor
- The probe trend plot can now operate over the currently visible region of the chromsome view
New in SeqMonk 0.15.0 (Jun 5, 2012)
- 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 0.14.0 (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
New in SeqMonk 0.13.0 (Jan 14, 2011)
- 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 (Jan 14, 2011)
- 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 (Jan 14, 2011)
- 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 0.10.2 (Jan 14, 2011)
- Fixed many bugs including:
- Spliced reads can now be imported without splitting and will span the proposed splice junction
- You can now extend reads and remove duplicates when using the generic text import
- Saving a project can now be cancelled safely
- Reports can now be cancelled and restarted correctly
- The cache indicator now shows when the cache is actually being used
- Many feauture mapping operations should be much quicker
New in SeqMonk 0.10.1 (Jan 14, 2011)
- 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
New in SeqMonk 0.10.0 (Jan 14, 2011)
- Made probes directional and added new visualisation and quantitation which uses this
- More support for removing or ignoring duplicate reads
- Option to extend single end reads to make analysing ChIP-Seq data easier
- Generic text import for features
- Added a genome annotation update mechanism
- New quantitation methods - enrichment quantitation and manual correction
- Import of bisulphite seq data mapped with bismark
- Improved speed when loading / saving projects
New in SeqMonk 0.9.1 (Jan 14, 2011)
- Fixed a bug in help when installed in a directory containing a space
- Fixed the ProbeList Probe Generator which was broken
- Check whether data is quantitated before launching views which require this
- Speed up switching between probe lists
- Add more validation to user supplied probe lists
New in SeqMonk 0.9 (Jan 14, 2011)
- ProbeLists are now heirarchical so you can follow how they were created
- Offical support for importing additional annotation
- Disk caching now caches annotation as well as reads
- Added an interstitial probe generator
- Added a probe length histogram
New in SeqMonk 0.8 (Jan 14, 2011)
- Added a disk cache mode to handle really big datasets
- Added a DataStore summary report
- Added a base pair quantitation
- Fixed the SAM parser to correctly assign strand information
- Updated and improved training course manual