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Revision history for ngs.plot.
==============================
2.61 November 13, 2015
- New Galaxy plug-in with re-designed GUI and some enhancements.
- Update ExtractGName.R to allow extraction of cluster information.
- Fix some gene ordering issue in km and hc.
- Remove the use of estiMapqStyle entirely to improve performance.
- Tiny bug fixes.
- Misc documentation improvements.
2.47 November 20, 2014
- Change default bam-pair colors to blue:yellow.
- Change bam-pair color from pair to tri.
- Add a parameter to control color distribution.
- Correct an error about "-N".
- Update plotCorrGram.r to fit the update of 'hclust'.
- Automatically determine if input is config or bam.
2.41 June 9, 2014
Major changes:
- Add rank-based normalization as a preprocessing step in clustering.
- Add K-means clustering.
- Add support for strand-specific sequencing data.
- Add support for paired-end sequencing data.
- Enhance the speed of RNA-seq coverage calculation by two folds.
- Allow enhancers and DHSs as additional features in a genomic database.
- Add a script to generate corrgrams between samples.
Minor changes:
- Remove PCA as a clustering method.
- Fix some permission and program argument issues that can cause problems
in galaxy installation.
- Fix a problem that custom bed files cannot be read in Galaxy.
- Explicitly create count files in current working directory, regardless
of bam file locations.
- Galaxy portability fix: remove hardcoded path from 'system' call.
- Fix STAR aligner 255 quality score issue.
- Add a function to automatically infer quality score style when the short
read aligner cannot be determined.
- Fix an issue of exception caused by quote or comment symbol in bed file.
- Remove the "remove zero profiles" function (which only causes confusion).
- Fix single gene plotting error, i.e. deal with the boundary cases where
the heatmap data contains only single gene.
- Add support for custom Y-axis scale.
- Adjust margin size in a heatmap according to font size.
- Adjust heatmap heights according to the actual number of regions to plot.
2.08 November 13, 2013
- Changed the pseudo-count calculation method in bam-pair. The new method
seems to give much better results in our tests.
- Corrected a bug that causes wrong matches when using a subset gene list
with genomes such as Yeast.
2.07 September 20, 2013
- Specify individual bed file for each bam file in configuration.
- Custom colors in configuration file
- Allow fragment length to be modified for each bam file.
- Adjust line width in replot.
- Sanity check for bed file.
- Misc. minor bugs fixed.
2.02 July 11, 2013
- Custom color scale for heatmap.
- Improved coverage calculation algorithm to make curves smoother.
- New bin-based approach to normalize coverage vectors(-AL bin).
- Options to turn on/off legend, figure box, axis labels and vertical
lines.
- Option to change font size in replot.
- List chromosome names in ngsplotdb.py.
- Correct an error that the vertical line does not align X-axis ticks
perfectly.
- Pattern match aligner programs.
- Minor changes to command line usage.
- Misc. minor bugs fixed.
- Moderate code refactoring.
2.00.1 June 19, 2013
- This is a bug fix version. ngs.plot v2.00 will emit error if you want to
use a BED file as genomic regions for plot. The bug has been fixed.
2.00 June 18, 2013
- Massive addition of support for other genomes such as rn5, mm10 and dm3
and other types of functional features like enhancers and dhs.
- We can now add support for any genome in UCSC or Ensembl within a short
time.
- A python script - ngsplotdb.py is developed to list installed genomes,
remove genomes or install new genomes.
- Ensemble is now the default database.
- Fixed a bug in plotting X-axis in avg. profiles introduced in v1.68.
- Allow mapping quality to be 0.
1.68 May 8, 2013
- Output gene order as shown in heatmap. Each replot will also generate a
new gene order.
- Allow users to change colors of heatmaps (replot).
- Added colorkey to heatmaps. You do not have to re-generate your plots,
use replot.r. Also allow a user to adjust scale at global, region and
local levels.
- Better sizing of figures and margins in heatmaps.
- Fixed a bug in X-axis plotting in heatmaps.
- Added a switch to integrate with Galaxy installation.
1.67.1 Apr 26, 2013
- Important bug fix: the heatmap does not follow the order of given gene
list even if "-GO none" is used. This has been fixed.
- New option "-RZ" to remove profiles that contain zero signal across all
positions and all NGS samples.
1.67 Apr 25, 2013
- Fixed a bug that may cause the program to exit when all mapping quality
values are NAs.
- Automatically convert mapping scores of 255 if bam files are converted
from BedTools.
- Fixed a bug that causes the program to exit when the flanking region
exceeds chromosomal start position in RNA-seq plotting.
- Added gene information to hmX.txt files.
- Misc. tiny bugs fixed.
1.66.2 Apr 4, 2013
- Fixed a bug that can cause RNA-seq plotting to exit with an error
message stating widths(x) cannot be negative.
1.66.1 Apr 3, 2013
- Fixed a bug that prevents replot from reading files correctly if the
original output name contains directory name.
1.66 Mar 26, 2013
- Added a function to accept bam file pairs.
- Automatically determine interval vs. flanking size in plot.
- Fixed a bug in RNA-seq coverage calculation (Thanks to Alphonse Chu from
Ottawa to point out).
- Minor bugs fixed.
1.65.1 Mar 18, 2013
- Fixed a bug that emits errors when using a custom bed file (Thanks to
Timothy E. Reddy from Duke to point out).
1.65 Mar 12, 2013
- This is an emergent bug fix version which addresses some problems when
reading bam header information.
- If alignment algorithm cannot be determined, ngs.plot will try to
automatically convert mapping scores of 255 to sth. meaningful.
- Uses a better way to read sequence names in a bam file.
- Buffer size is automatically set based on fragment length.
1.64 Mar 7, 2013
- Significant improvement to coverage calculation. The program now
calculate coverage based on needs by extracting bam files on the go.
This has significantly reduced memory requirement.
- cov.calc.r has been removed from the package. There is no need to pre-
calculate coverage any more.
- replot.r now supports heatmap and a few other options to tune figures.
- The result files are now wrapped as a zip file for cleaness.
1.34 Feb 23, 2013
- A lot of code re-writing to optimize performance and to modularize the
project.
- More usage of parallel processing.
- Added new heatmap function.
- Implemented 6 algorithms to order genes in heatmaps.
- Added column subset function in replot.r.
- Used robust statistics as default for avg. profile plot.
- Reconstruction of the gene database and speedup annotation loading by ~6
folds.
1.05 Dec 3, 2012
- Fix bugs in calculating physical coverage
- Fix bugs in the scripts that are used to extract exons from Cufflinks.
1.04 Nov 12, 2012
- Automatic turning off SEM when there is only single gene given in gene
list.
- Misc. re-organization of ngs.plot.r code.
- Some re-organization of distribution folder.
- Added example gene list; example data for user to run through.
- Added script "alt_reg_cufflinks" which extracts all alternative regions
in one command.