Ecosyste.ms: Issues

An open API service for providing issue and pull request metadata for open source projects.

GitHub / kharchenkolab/pagoda2 issues and pull requests

#147 - Error in extendedP2proc

Issue - State: closed - Opened by vixenk 2 months ago - 1 comment

#146 - pagoda2WebApp_readStaticFile function does not work

Issue - State: closed - Opened by Auryllius 3 months ago - 4 comments

#145 - 'as_cholmod_sparse' not provided by package 'Matrix'

Issue - State: closed - Opened by IENAUMANN 7 months ago - 2 comments

#144 - Application to bulk-seq data?

Issue - State: closed - Opened by hsiowa2 9 months ago - 1 comment

#143 - Keep limits fix

Pull Request - State: closed - Opened by rrydbirk about 1 year ago - 2 comments

#142 - Mat::init(): requested size is too large; suggest to enable ARMA_64BIT_WORD

Issue - State: closed - Opened by wresch over 1 year ago - 10 comments

#141 - 'mc.cores' > 1 is not supported on Windows

Issue - State: closed - Opened by cfz1998 over 1 year ago - 2 comments

#140 - Report a small bug

Issue - State: closed - Opened by Junedays almost 2 years ago - 7 comments

#139 - keep.limits triggers error in plotEmbedding

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

#138 - Updates for Matrix 1.4.2

Pull Request - State: closed - Opened by evanbiederstedt about 2 years ago

#137 - Error in hdea

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

#136 - Extract pathway overdispersion data on a per cell basis

Issue - State: closed - Opened by chrisley90 over 2 years ago - 5 comments

#135 - Error in extendedP2proc

Issue - State: closed - Opened by Dimmiso over 2 years ago - 6 comments

#134 - Error in extendedP2proc

Issue - State: closed - Opened by Wangxin555 over 2 years ago - 1 comment

#133 - An error about running show.app in vignette

Issue - State: closed - Opened by rocketeer1998 over 2 years ago - 12 comments

#131 - Running Overdispersion Pathway Analysis

Issue - State: closed - Opened by airfan0 over 2 years ago - 2 comments

#130 - installing problem

Issue - State: closed - Opened by ch8316f5eyu over 2 years ago - 1 comment

#129 - Trying to run Pagoda2 on Seurat pre-processed data

Issue - State: closed - Opened by airfan0 over 2 years ago - 3 comments

#128 - Exporting lists of genesets within aspects

Issue - State: closed - Opened by BW093 almost 3 years ago - 4 comments

#127 - read10xMatrix error

Issue - State: closed - Opened by gengnomes almost 3 years ago - 5 comments

#126 - testPathwayOverdispersion returns NA

Issue - State: closed - Opened by duocang about 3 years ago - 4 comments

#125 - Version 1.0.5

Pull Request - State: closed - Opened by evanbiederstedt about 3 years ago

#124 - Remove vignettes

Pull Request - State: closed - Opened by evanbiederstedt about 3 years ago

#123 - Could not find function "n2Knn"

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

#122 - Error in extendedP2proc

Issue - State: closed - Opened by markdunning over 3 years ago - 2 comments

#121 - Unable to view genes associated with GO terms

Issue - State: closed - Opened by n1tian over 3 years ago - 2 comments

#120 - mc.cores >1 not supported on Windows

Issue - State: closed - Opened by markdunning over 3 years ago - 2 comments

#119 - batch

Issue - State: closed - Opened by b1lake over 3 years ago - 5 comments
Labels: bug

#118 - Version 1.0.0 on CRAN

Pull Request - State: closed - Opened by evanbiederstedt over 3 years ago

#116 - read.10x.matrices() - Error with Cell Ranger v3.x data

Issue - State: closed - Opened by AmelZulji over 3 years ago - 14 comments

#115 - cannot change value of locked binding for 'counts'

Issue - State: closed - Opened by xiongyichun over 3 years ago - 8 comments

#114 - Version 1.0.0

Pull Request - State: closed - Opened by evanbiederstedt over 3 years ago

#113 - fac2col not found

Issue - State: closed - Opened by cstubben almost 4 years ago - 7 comments

#112 - Use R6 class for Pagoda2 class

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

#111 - Set openmp conditionals for #pragma omp

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

#110 - adjustVariance "fatal error" in R

Issue - State: closed - Opened by haircell almost 4 years ago - 11 comments

#109 - Version 0.1.3

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

#108 - macOS CMD build error (installation issue)

Issue - State: closed - Opened by haircell almost 4 years ago - 12 comments

#107 - Install on Windows

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 1 comment

#106 - use lambda expression in Hnsw::NormalizeVector

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#105 - Remove unused/outdated functions

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 3 comments

#104 - simply change axes from log10 to log, adjustVariance

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 1 comment

#103 - scale by log10(exp(1)) for log10 plots

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

#102 - source code should use TRUE/FALSE

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#101 - clarifying log, log10

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 2 comments

#100 - remove mapply from factorListToMetadata

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 3 comments

#99 - remove test.stability, update documentation

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#98 - Bugfix, check list elements exist within serializeToStaticFast(), WriteListToBinary()

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 2 comments

#97 - Add biocViews in DESCRIPTION

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago - 1 comment

#96 - colorRamps used in the vignettes, added to Suggests

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#95 - added wiki to README, Mac OS installation

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#94 - License revisions for R packages

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#93 - Bugfix/rcpp rcout

Pull Request - State: closed - Opened by evanbiederstedt about 4 years ago

#92 - Error: no method for coercing this S4 class to a vector

Issue - State: closed - Opened by KabitaBaral1 over 4 years ago - 1 comment

#91 - scanpy h5ad to pagoda2 object(s)

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

#90 - GitHub connection error during installation

Issue - State: closed - Opened by xuebaliang over 4 years ago - 3 comments

#89 - Nothing happens after install_github("hms-dbmi/pagoda2")

Issue - State: closed - Opened by kaizen89 over 4 years ago - 2 comments

#88 - Web browser kills pagoda2WebApp when doing DE on large datasets

Issue - State: closed - Opened by GMaciag about 5 years ago - 4 comments
Labels: help wanted

#87 - pagoda2 compare samples

Issue - State: closed - Opened by SBata over 5 years ago - 1 comment

#86 - where is the entire document?

Issue - State: closed - Opened by wJDKnight over 5 years ago - 1 comment

#85 - Embedding issue in GetDensityClusters

Issue - State: closed - Opened by vkorobeynyk over 5 years ago - 1 comment

#84 - Progress bars for extendedP2proc()

Pull Request - State: closed - Opened by rrydbirk over 5 years ago - 4 comments

#83 - extendedP2proc hanging on "determining valid pathways"

Issue - State: closed - Opened by rrydbirk over 5 years ago - 9 comments

#82 - Normalized Counts Units

Issue - State: closed - Opened by drneavin over 5 years ago - 1 comment

#81 - subtract aspect

Issue - State: closed - Opened by PavelnZ over 5 years ago - 1 comment

#79 - makeKnnGraph crashes with: "address 0x2b0055be820c, cause 'illegal operand' "

Issue - State: closed - Opened by rlittman16 over 5 years ago - 1 comment

#78 - Installation problem

Issue - State: closed - Opened by kunUCSD over 5 years ago - 9 comments

#77 - fix slow serialize

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

#76 - Creating a single pagoda2 object from multiple count matrices

Issue - State: closed - Opened by kiter2520 over 5 years ago - 2 comments

#71 - Can't add custom sets of marker genes

Issue - State: closed - Opened by mariafiruleva almost 6 years ago

#67 - Memory allocation error during t-SNE embedding for large datasets

Issue - State: closed - Opened by VPetukhov almost 6 years ago - 4 comments
Labels: enhancement

#64 - Pagoda2 not compiling

Issue - State: closed - Opened by stela2502 about 6 years ago - 3 comments

#63 - Installation failed on a test stage.

Issue - State: closed - Opened by pavelmor about 6 years ago - 3 comments

#62 - Add walktrap clustering to pagoda with option to specify number of clusters

Issue - State: closed - Opened by VPetukhov about 6 years ago - 2 comments
Labels: enhancement

#60 - Update Makevars

Pull Request - State: closed - Opened by Simontuk about 6 years ago - 5 comments

#59 - Highlight cell subsets being compared on diff. expression result heatmap

Issue - State: closed - Opened by pkharchenko about 6 years ago - 1 comment
Labels: enhancement

#58 - subset data based on clusters

Issue - State: closed - Opened by DRLaks about 6 years ago - 1 comment

#56 - T-SNE fails because of duplicates in cell coordinates

Issue - State: closed - Opened by Chlamidomonas about 6 years ago - 2 comments

#55 - Use faster methods for pairwise correlation

Issue - State: closed - Opened by VPetukhov about 6 years ago - 1 comment
Labels: enhancement

#54 - web app doesn't show GO pathways related to aspects

Issue - State: closed - Opened by elimereu about 6 years ago - 4 comments

#51 - Possibly wrong axis labels for the plot generated by `$adjustVariance`

Issue - State: closed - Opened by mt1022 over 6 years ago - 1 comment

#50 - how to control cluster numbers?

Issue - State: closed - Opened by lixin4306ren over 6 years ago - 3 comments

#48 - Web App hangs when running DE on old file

Issue - State: closed - Opened by barkasn over 6 years ago - 1 comment
Labels: bug

#42 - test.stability parameter in getKnnClusters breaks web app visualization

Issue - State: closed - Opened by VPetukhov over 6 years ago - 8 comments

#41 - Create LICENSE

Pull Request - State: closed - Opened by barkasn over 6 years ago

#40 - Remove forgotten hnswKnnLp function from nmslib

Pull Request - State: closed - Opened by VPetukhov over 6 years ago

#39 - Installation problem

Issue - State: closed - Opened by zhengrongbin over 6 years ago - 6 comments

#38 - Error in adjustVariance

Issue - State: closed - Opened by dalhoomist over 6 years ago - 2 comments

#36 - Ordering web apps by non-default groups doesn't work

Issue - State: closed - Opened by barkasn over 6 years ago
Labels: bug

#33 - plotEmbedding() crashes

Issue - State: closed - Opened by barkasn almost 7 years ago - 1 comment

#30 - Rcpp code uses std::cout

Issue - State: closed - Opened by barkasn almost 7 years ago - 1 comment
Labels: enhancement

#27 - What is the underlying method for correcting batch effect in pagoda2?

Issue - State: closed - Opened by ahy1221 almost 7 years ago - 2 comments

#25 - Core functionality is undocumented

Issue - State: closed - Opened by barkasn almost 7 years ago - 3 comments

#24 - Regex selection of cell on the web interface doesn't work

Issue - State: closed - Opened by barkasn almost 7 years ago - 1 comment
Labels: bug

#23 - Multicore tSNE calculation issue

Issue - State: closed - Opened by barkasn almost 7 years ago - 2 comments
Labels: enhancement

#22 - makeKnnGraph() crashes if the specified embedding doesn't exist

Issue - State: closed - Opened by barkasn almost 7 years ago

#18 - biomaRt custom annotation

Issue - State: closed - Opened by TsukasaKo about 7 years ago - 2 comments