NEWS
fishpond 2.8.0
- Corrected a bug in the two-group interaction (without pairing)
functionality, when the groups were imbalanced, as identified by
Samuel Chen. Fixes GitHub issue #35.
fishpond 2.7.1
- Corrected a bug in the two-group interaction (without pairing)
functionality, when the groups were imbalanced, as identified by
Samuel Chen. Fixes GitHub issue #35.
fishpond 2.5.4
- As CellRanger 7 includes both spliced and unspliced counts in their
count matrix, we want to mimic this behavior by adding more
pre-defined output formats in the loadFry function. We added "all"
and "U+S+A" to include all counts in the count matrix. Moreover, now
the "scRNA" output format has an "unspliced" field, which contains
the unspliced count matrix.
fishpond 2.5.3
- Fix bug where salmonEC did not correct equivalence class
names for going from 0-indexing to 1-indexing internally. In prior
versions, to correctly link equivalence classes to gene names,
users would have needed to manually add a value of 1 to the
equivalence class names, which was erroneously not mentioned
in the man files. After this bug fix, if the equivalence class
identifier reads 1|2|8, then the equivalence class is immediatly
compatible with the transcripts and their respective genes in rows
1, 2 and 8 of 'tx2gene_matched', without any further user
intervention.
fishpond 2.5.1
- Fix plotAllelicGene() so that when samples have an allele
with no expression at the gene level, it doesn't throw
an error trying to divide by 0.
fishpond 2.4.0
- For simple paired swish analysis, adding a
fast=1 method
which uses a one-sample z-score on the paired LFCs
(averaged over samples, then median over inferential
replicates). The permutation is computed by changing the
signs of the LFC matrix and recomputing z-scores.
Testing on the vignette example, but using all the transcripts,
the one-sample z-score method takes < 20 seconds while the
signed rank method takes > 200 seconds (12x speedup),
while they have a high rate of agreement on the detected set
(30:1 in common vs discordant).
- Removed the fast=0 methods that were previously implemented
where ranks could optionally be recomputed for every
permutation. This was much slower and didn't have any
appreciable benefit.
- readEDS() has moved to the
eds package, such that
fishpond no longer requires Rcpp and C++ code compilation.
- Fix bug identified by GitHub user @JosephLalli, where
importAllelicCounts would find a1 and a2 strings
internal to gene IDs, instead of at the suffix.
fishpond 2.3.22
- Fix bug identified by GitHub user @JosephLalli, where
importAllelicCounts would find a1 and a2 strings
internal to gene IDs, instead of at the suffix.
fishpond 2.3.14
- For simple paired swish analysis, adding a
fast=1 method
which uses a one-sample z-score on the paired LFCs
(averaged over samples, then median over inferential
replicates). The permutation is computed by changing the
signs of the LFC matrix and recomputing z-scores.
Testing on the vignette example, but using all the transcripts,
the one-sample z-score method takes <20 seconds while the
signed rank method takes >200 seconds (12x speedup),
while they have a high rate of agreement on the detected set (
30:1 in common vs discordant).
- Removed the fast=0 methods that were previously implemented
where ranks could optionally be recomputed for every
permutation. This was much slower and didn't have any
appreciable benefit.
fishpond 2.3.7
- readEDS() has moved to the
eds package.
fishpond 2.2.0
- New vignette demonstrating allelic analysis at isoform,
TSS, or gene-level. See more details below.
- New import functions for equivalence class analysis of Salmon
or alevin data, written by Jeroen Gilis. See salmonEC() and
alevinEC() man pages.
- New plotAllelicGene() and plotAllelicHeatmap() functions
for plotting results from allelic expression analysis.
- New makeTx2Tss() helper function for allelic analysis.
- Now importFromAllelicCounts() can take a GRanges
object as the
tx2gene argument, so that ranges will
be distributed to the rowRanges of the output
SummarizedExperiment.
- Adding
shiftX argument to plotInfReps() for numeric
x variable, to help with overplotting.
- Re-organized package for new pkgdown homepage:
https://mikelove.github.io/fishpond
fishpond 2.0.0
- New loadFry() function, written by Dongze He with
contributions from Steve Lianoglou and Wes Wilson.
loadFry() helps users to import and process
alevin-fry quantification results. Can process
spliced, unspliced and ambiguous counts separately
and flexibly. Has specific output formats designed
for downstream use with scVelo or velocity analysis.
See ?loadFry for more details.
- Adding correlation tests: Spearman or Pearson
correlations of a numeric covariate with the
log counts, or with the log fold changes across
pairs. The Spearman correlation test with counts
was already implemented in the original SAMseq
method as response type = "Quantitative".
For new functionality see 'cor' argument in the
?swish man page.
- Adding importAllelicCounts() to facilitate importing
Salmon quantification data against a diploid
transcriptome. Can import either as a 'wide'
format or as 'assays'. Leverages tximeta().
For gene-level summarization, importAllelicCounts()
can create an appropriate tx2gene table
with the necessary a1 and a2 suffices,
and it will automatically set txOut=FALSE, see
?importAllelicCounts for more details.
- Added a 'q' argument to plotInfReps to change the
intervals when making point and line plots.
- Switched the legend of plotInfReps so that
reference levels will now be on the bottom,
and non-reference (e.g. treatment) on top.
fishpond 1.99.18
- Added helper functionality to importAllelicCounts,
so it will create an appropriate tx2gene table
with the necessary a1 and a2 suffices,
and it will automatically set txOut=FALSE.
- Added a 'q' argument to plotInfReps to change the
intervals when making point and line plots.
- Switched the legend of plotInfReps so that
reference levels will now be on the bottom,
and non-reference (e.g. treatment) on top.
- Added loadFry() to process alevin-fry
quantification result. Can process spliced,
unspliced and ambiguous counts separately
and flexibly.
fishpond 1.99.15
- Adding correlation tests: Spearman or Pearson
correlations of a numeric covariate with the
log counts, or with the log fold changes across
pairs. The Spearman correlation test with counts
was already implemented in the original SAMseq
method as response type = "Quantitative".
For new functionality see 'cor' argument in the
?swish man page.
- Adding importAllelicCounts() to facilitate importing
Salmon quantification data against a diploid
transcriptome. Can import either as a 'wide'
format or as 'assays'. Leverages tximeta().
fishpond 1.9.6
- Specifying ties.method in matrixStats::rowRanks.
fishpond 1.9.1
- Added importAllelicCounts() with options for importing
Salmon quantification on diploid transcriptomes.
fishpond 1.8.0
- Added note in vignette about how to deal with estimated
batch factors, e.g. from RUVSeq or SVA. Two strategies are
outlined: either discretizing the estimate batch factors
and performing stratified analysis, or regressing out the
batch-associated variation using limma's removeBatchEffect.
Demonstation code is included.
fishpond 1.6.0
- Added makeInfReps() to create pseudo-inferential replicates
via negative binomial simulation from mean and variance
matrices. Note: the mean and the variance provide the
inferential distribution per element of the count matrix.
See preprint for details, doi: 10.1101/2020.07.06.189639.
- Added splitSwish() and addStatsFromCSV(), which can be used
to distribute running of Swish across a number of jobs
managed by
Snakemake. See vignette for description of
a suggested workflow. For a large single-cell dataset
with mean and variance summaries of inferential uncertainty,
splitSwish() avoids generating the inferential replicate
counts until the data has been split into smaller pieces and
sent to different jobs, then only the necessary summary
statistics are gathered and q-values computed by
addStatsFromCSV().
- plotInfReps() gains many new features to facilitate plotting of
inferential count distributions for single cells, as quantified
with alevin and imported with tximport. E.g. allow for numeric
x argument plus grouping with cov for showing
counts over pseudotime across groups of cells. Also added
applySF argument which can be used to divide out a
size factor, and the reorder argument which will re-order
the samples/cells within groups by the count. plotInfReps()
will draw boxplots with progressively thinner visual features
as the number of cells grows to make the plots still legible.
fishpond 1.5.2
- First version of makeInfReps(), to create pseudo-infReps
via negative binomial simulation from set of mean and
variance matrices in the assays of the SummarizedExperiment.
fishpond 1.4.0
- Added isoformProportions(), which can be run after
scaleInfReps() and optionally after filtering out
transcripts using labelKeep(). Running swish() after
isoformProportions() will produce differential transcript
usage (DTU) results, instead of differential transcript
expression (DTE) results. Example in vignette.
- Default number of permutations increased from 30 to 100.
It was observed that there was too much fluctuation in the
DE called set for nperms=30 across different seeds, and
setting to 100 helped to stabilize results across seeds,
without increasing running time too much. For further reduced
dependence on the seed, even higher values of nperms
(e.g. 200, 300) can be used.
fishpond 1.3.8
- Added isoformProportions(), which can be run after
scaleInfReps() and optionally after filtering out
transcripts using labelKeep(). Running swish() after
isoformProportions() will produce differential transcript
usage (DTU) results, instead of differential transcript
expression (DTE) results. Example in vignette.
fishpond 1.3.4
- Default number of permutations increased from 30 to 100.
It was observed that there was too much fluctuation in the
DE called set for nperms=30 across different seeds, and
setting to 100 helped to stabilize results across seeds,
without increasing running time too much. For further reduced
dependence on the seed, even higher values of nperms
(e.g. 200, 300) can be used.
fishpond 1.2.0
- Switching to a faster version of Swish which only
computes the ranks of the data once, and then re-uses
this for the permutation distribution. This bypasses
the addition of uniform noise per permutation and
is 10x faster. Two designs which still require
re-computation of ranks per permutation are the
paired analysis and the general interaction analysis.
Two-group, stratified two-group, and the paired
interaction analysis now default to the new fast
method, but the original, slower method can be used
by setting fast=0 in the call to swish().
- Adding Rcpp-based function readEDS() written by
Avi Srivastava which imports the sparse counts stored
in Alevin's Efficient Data Storage (EDS) format.
- Changed the vignette so that it (will) use a linkedTxome,
as sometime the build would break if the Bioc build
machine couldn't access ftp.ebi.ac.uk.
- Add 'computeInfRV' function. InfRV is not used in the
Swish methods, only for visualization purposes in the
Swish paper.
- removed 'samr' from Imports, as it required source
installation, moved to Suggests, for optional qvalue
calculation
fishpond 0.99.30
- added two interaction tests, described in ?swish
- incorporate qvalue package for pvalue, locfdr and qvalue
- added plotMASwish() to facilitate plotting
- wilcoxP is removed, and the mean is used instead
fishpond 0.99.0
- fishpond getting ready for submission to Bioc