lpantano/DEGreport issues and pull requests

#66 - Connecting dots and lines in degPlotCluster()

Issue - State: open - Opened by CroixJeremy2 about 1 month ago - 1 comment

#65 - New genes that did not exist in dds object suddenly showed up after degPatterns

Issue - State: open - Opened by sandray-imp 6 months ago - 1 comment

#64 - Clarification with degMerge function

Issue - State: open - Opened by Chengyao-Peng 6 months ago - 1 comment

#63 - `scale` parameter is missing in `degPCA`

Issue - State: closed - Opened by bounlu 9 months ago - 1 comment

#62 - degPatterns crashes because of stack overloading

Issue - State: closed - Opened by NastiaSkuba 10 months ago - 9 comments

#61 - matching sequence of dend clusters to trajectory clusters

Pull Request - State: closed - Opened by zellerivo 10 months ago - 1 comment

#60 - Error in DEGpatterns: could not find function "set"

Issue - State: closed - Opened by gowgowuk 10 months ago - 11 comments

#59 - How does degPatterns() decide what height to use for cutting tree

Issue - State: closed - Opened by sang-15 12 months ago - 1 comment

#58 - degCovariates does not shade by r value

Issue - State: closed - Opened by hwick about 1 year ago - 5 comments

#57 - issues with degPatterns not setting Time in Normalize

Issue - State: closed - Opened by kesner over 1 year ago - 8 comments

#56 - new features: dendogram as output and specifying number of desired clusters

Pull Request - State: closed - Opened by zellerivo over 1 year ago - 6 comments

#55 - Boxplot position

Issue - State: closed - Opened by Chunhuixu almost 2 years ago - 1 comment

#54 - Fixed missing sticker image link

Pull Request - State: closed - Opened by Matt-Int almost 2 years ago

#53 - `lasso2` dependency no longer on CRAN

Issue - State: closed - Opened by kennyworkman about 2 years ago - 5 comments

#52 - Regarding Clustering Based on Expression Pattern

Issue - State: closed - Opened by drives28 about 2 years ago - 1 comment

#51 - Regarding Group # from degPatterns Output

Issue - State: closed - Opened by drives28 about 2 years ago - 2 comments

#50 - Add batchx data

Pull Request - State: closed - Opened by idelvall over 2 years ago

#49 - Validate the clusters from degPatterns

Issue - State: closed - Opened by lgallegovillar almost 3 years ago - 2 comments

#48 - Sort each cluster graph numerically

Issue - State: closed - Opened by bacas2 almost 3 years ago - 1 comment

#47 - Extracting Gene-Gene distance matrix from DegPatterns

Issue - State: closed - Opened by chk63 about 3 years ago - 3 comments

#46 - Extract One Cluster Plot from degPlotCluster

Issue - State: closed - Opened by drives28 over 3 years ago - 3 comments

#45 - Show Expression Changes from One Cluster

Issue - State: closed - Opened by drives28 over 3 years ago - 5 comments

#44 - z-scores of gene abudance

Issue - State: closed - Opened by RubenRBakker over 3 years ago - 10 comments

#43 - lasso2 is an R4 only package

Issue - State: closed - Opened by alpapan over 3 years ago - 1 comment

#42 - Plot shows only one coldata group on x-axis

Issue - State: closed - Opened by elcega almost 4 years ago - 3 comments

#41 - Extract the genes of each group pattern

Issue - State: closed - Opened by elcega almost 4 years ago - 3 comments

#40 - Error in install.packages : ERROR: failed to lock directory

Issue - State: closed - Opened by venuraherath almost 4 years ago - 1 comment

#39 - Error in rep("one_group", nrow(metadata)) : invalid 'times' argument

Issue - State: closed - Opened by elcega almost 4 years ago - 8 comments

#38 - Point size fix

Pull Request - State: closed - Opened by vbarrera almost 4 years ago

#37 - Problem with `summarise()`

Issue - State: closed - Opened by Bithorax almost 4 years ago - 4 comments

#36 - `degCovariates`: breaking change in dplyr filter code

Issue - State: open - Opened by mjsteinbaugh over 4 years ago - 6 comments

#35 - How to re-cluster in each group for DEGpattern?

Issue - State: open - Opened by ShaowenJ over 4 years ago

#34 - Wrong clusters identification

Issue - State: closed - Opened by jgarces02 over 4 years ago - 2 comments

#33 - Can we order the top N genes within degplot

Issue - State: open - Opened by klai001 over 4 years ago - 5 comments

#32 - degCovariates ERROR

Issue - State: open - Opened by algilm over 4 years ago - 1 comment

#31 - How is variance explained calculated for degCovariates?

Issue - State: closed - Opened by Zepeng-Mu over 4 years ago - 2 comments

#30 - error message

Issue - State: open - Opened by NextGenBioinformatics over 4 years ago - 1 comment

#29 - Add prefix to the title plot

Issue - State: open - Opened by lpantano over 4 years ago

#28 - degPatterns results exists unsimilar pattern in a cluster

Issue - State: open - Opened by etbuface about 5 years ago - 1 comment

#27 - degPatterns error

Issue - State: closed - Opened by wangmhan about 5 years ago - 8 comments

#26 - Incorrect reordering of TimeSeries in degPattern

Issue - State: closed - Opened by sum732 over 5 years ago - 2 comments

#25 - bug in degPlotWide() (v. 1.18.1) only works if group="group"

Issue - State: closed - Opened by hexaflexa over 5 years ago - 2 comments

#24 - Fix for missing factor observations when summarizing in DEGpattern

Pull Request - State: closed - Opened by roryk over 5 years ago

#23 - degCheckFactors error

Issue - State: open - Opened by maria-xi over 5 years ago - 4 comments

#22 - Fix typos in degPattern message.

Pull Request - State: closed - Opened by roryk about 6 years ago - 4 comments

#21 - Check class

Issue - State: closed - Opened by lpantano about 7 years ago
Labels: bug, internal

#20 - Adapt DEGSet to limma output

Issue - State: open - Opened by lpantano about 7 years ago
Labels: internal, analysis

#19 - Adapt plots to handle DEGSet class

Issue - State: closed - Opened by lpantano about 7 years ago
Labels: enhancement, internal

#18 - Add method to get data.frame table

Issue - State: closed - Opened by lpantano about 7 years ago
Labels: enhancement, internal

#17 - move NEWS to parent directory

Issue - State: closed - Opened by lpantano about 7 years ago
Labels: internal

#16 - Add DEGresults examples to vignette

Issue - State: open - Opened by lpantano about 7 years ago
Labels: bug, internal

#15 - Clean data to use in example

Issue - State: closed - Opened by lpantano about 7 years ago
Labels: bug, internal

#14 - Migrate to testthat

Issue - State: closed - Opened by lpantano about 7 years ago
Labels: bug, internal

#13 - Correct if statement and problem with batch label

Pull Request - State: closed - Opened by vbarrera about 7 years ago - 2 comments

#12 - NAMESPACE with roxygen2

Issue - State: closed - Opened by lpantano over 7 years ago
Labels: bug, internal

#11 - degPCA to have only ma as input

Issue - State: open - Opened by lpantano over 7 years ago
Labels: enhancement, plots

#10 - add pvalue to degCovariates

Issue - State: closed - Opened by lpantano over 7 years ago
Labels: enhancement, plots

#9 - add function for PCA vs metadata correlation

Issue - State: closed - Opened by lpantano over 7 years ago - 1 comment
Labels: enhancement, analysis

#8 - add function for co-expression analyais glbio17

Issue - State: open - Opened by lpantano over 7 years ago - 1 comment
Labels: enhancement, analysis

#7 - Add custom labels to the plot

Pull Request - State: closed - Opened by vbarrera over 7 years ago

#6 - added as.factor() to batch for numerical batches

Pull Request - State: closed - Opened by vbarrera almost 8 years ago - 1 comment

#5 - Remove logging as a dependency.

Pull Request - State: closed - Opened by roryk about 8 years ago - 3 comments

#4 - change file for string as jags input

Issue - State: closed - Opened by lpantano over 9 years ago - 1 comment
Labels: enhancement

#3 - change axis labels to make it clear

Issue - State: closed - Opened by lpantano almost 10 years ago
Labels: enhancement

#2 - rjags removal and sampling fix

Pull Request - State: closed - Opened by roryk almost 10 years ago - 3 comments

#1 - add glm models

Issue - State: open - Opened by lpantano about 10 years ago

GitHub / lpantano/DEGreport issues and pull requests