/usr/lib/R/site-library/EBSeq/NEWS is in r-bioc-ebseq 1.18.0-1.
This file is owned by root:root, with mode 0o644.
The actual contents of the file can be viewed below.
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 | CHANGES IN VERSION 1.11.1
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o Fixed a bug in EBTest() which may cause error when performing isoform DE testing 1 sample vs. multiple samples.
CHANGES IN VERSION 1.9.3
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o Correct typos in GetDEResults help file.
o Include an alternative method for normalization. The alternative method is similar to median-by-ratio normalization,
but can deal with the cases when all of the genes/isoforms have at least one zero counts (in which case the
median-by-ratio normalization will fail). This alternative method is developed for single-cell RNA-seq analysis
where the dataset always contains a large amount of zeros.
CHANGES IN VERSION 1.9.2
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o Fixed a bug which may cause error when input a matrix to the sizeFactors parameter
CHANGES IN VERSION 1.9.1
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o Added Q&A seqction in vignette to address common questions
CHANGES IN VERSION 1.7.1
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o In EBSeq 1.7.1, EBSeq incorporates a new function
GetDEResults() which may be used to obtain a list of transcripts under a target FDR
in a two-condition experiment.
The results obtained by applying this function with its default setting will be
more robust to transcripts with low variance and potential outliers.
By using the default settings in this function,
the number of genes identified in any given analysis may
differ slightly from the previous version (1.7.0 or order).
To obtain results that are comparable
to results from earlier versions of EBSeq (1.7.0 or older), a user may set
Method="classic" in GetDEResults() function, or use the original GetPPMat() function.
The GeneDEResults() function also allows a user to modify thresholds to
target genes/isoforms with a pre-specified posterior fold change.
o Also, in EBSeq 1.7.1, the default settings in EBTest() and EBMultiTest() function
will only remove transcripts with all 0's (instead of removing transcripts with
75th quantile less than 10 in version 1.3.3-1.7.0).
To obtain a list of transcripts comparable to the results generated by
EBSeq version 1.3.3-1.7.0, a user may change Qtrm = 0.75 and QtrmCut = 10
when applying EBTest() or EBMultiTest() function.
CHANGES IN VERSION 1.5.4
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o An extra numerical approximation step is implemented
in EBMultiTest() function to avoid
underflow. The underflow is likely due to large number of samples.
A bug in EBMultiTest() is fixed. The bug will cause error when there is
exactly 1 gene/isoform that needs numerical approximation.
CHANGES IN VERSION 1.5.3
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BUG FIXES
o Fixed a bug that may generate NA FC estimates when there are no replicates.
CHANGES IN VERSION 1.5.2
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NEW FEATURES
o An extra numerical approximation step is
implemented in EBTest() function to avoid
underflow. The underflow is likely due to large number of samples.
CHANGES IN VERSION 1.3.3
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NEW FEATURES
o In EBSeq 1.3.3, the default setting of EBTest function will remove
low expressed genes (genes whose 75th quantile of normalized counts is less
than 10) before identifying DE genes.
These two thresholds can be changed in EBTest function.
Because low expressed genes are disproportionately noisy,
removing these genes prior to downstream analyses can improve model fitting and increase robustness
(e.g. by removing outliers).
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