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
#132 - Error in lm.fit(x, y, offset = offset, singular.ok = singular.ok, ...) : 0 (non-NA) cases
Issue -
State: closed - Opened by Telogen over 2 years ago
- 1 comment
#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
#117 - Error in gzfile(file, mode) : cannot open the connection at testPathwayOverdispersion
Issue -
State: closed - Opened by mzhibo over 3 years ago
- 2 comments
#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
#80 - Error in setCountMatrix(x, min.cells.per.gene = min.cells.per.gene, trim = trim, : duplicate gene names are not allowed - please reduce
Issue -
State: closed - Opened by wupeng2 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