Ecosyste.ms: Issues

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

GitHub / kharchenkolab/conos issues and pull requests

#137 - Update integrations.R

Pull Request - State: open - Opened by shivangsharma 4 months ago - 5 comments

#136 - Using SCT assays

Issue - State: closed - Opened by mckoch234 8 months ago - 6 comments

#135 - Adding MetaData to Conos Object

Issue - State: closed - Opened by mckoch234 8 months ago - 1 comment

#134 - Attaching metadata from Seurat Objects

Issue - State: closed - Opened by aliibarry about 1 year ago - 1 comment
Labels: help wanted

#133 - Prepare for upcoming Seurat v5 release

Issue - State: open - Opened by saketkc over 1 year ago - 1 comment
Labels: help wanted

#132 - Integration of multi-modal data based on a joint space

Issue - State: open - Opened by VPetukhov almost 2 years ago
Labels: enhancement, help wanted

#131 - Feeding output from getPerCellTypeDE into Heatmap

Issue - State: open - Opened by Dimmiso about 2 years ago - 2 comments

#129 - largeVis embedding does not utilize n.cores argument

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

#128 - why I can't find the "velocityInfoConos" function in conos(v1.4.6)?

Issue - State: closed - Opened by liuyang218622 over 2 years ago - 5 comments

#127 - Updates for Matrix 1.4.2

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

#125 - How to get predicted cell types?

Issue - State: closed - Opened by Kevis9 over 2 years ago - 2 comments

#124 - Running Conos functions across multiple nodes/computers

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

#123 - Rstudio session crash when making Conos object (LeidenAlg cluster estimation)

Issue - State: closed - Opened by FFriis almost 3 years ago - 11 comments

#122 - findSubcommunities

Issue - State: closed - Opened by Laura19993 almost 3 years ago - 7 comments

#121 - shared NN variant of $buildGraph

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

#120 - getDifferentialGenes for selected groups?

Issue - State: closed - Opened by Dimmiso almost 3 years ago - 6 comments

#119 - conos install error igraph.so not found

Issue - State: closed - Opened by tedtoal almost 3 years ago - 16 comments

#118 - 'adjustedRand not in load table'

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

#117 - docker build fails

Issue - State: closed - Opened by EugeneEA about 3 years ago - 1 comment

#116 - Cell subsetting error

Issue - State: closed - Opened by hiraksarkar about 3 years ago - 4 comments
Labels: bug, help wanted

#115 - Downsample from each cluster

Issue - State: open - Opened by hiraksarkar about 3 years ago - 3 comments
Labels: enhancement, help wanted

#114 - Wrong legend while using custom palette

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

#113 - Redundant Suggests after transfer to sccore

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

#112 - Update walkthrough

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

#111 - Passing Leiden or Walktrap clusters to plotDEheatmap

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

#110 - Version 1.4.3

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

#109 - Allow embedding parameter to be case insensitive

Pull Request - State: closed - Opened by evanbiederstedt over 3 years ago - 2 comments

#108 - con$plotGraph(embedding = [X]) appears to be case sensitive

Issue - State: closed - Opened by ACastanza over 3 years ago - 15 comments

#107 - Fix parseCellGroups() to check if clustering exists

Pull Request - State: closed - Opened by evanbiederstedt over 3 years ago - 1 comment

#106 - [Feature Request] Support for scVelo structured h5ad files for velocity-conos

Issue - State: open - Opened by ACastanza over 3 years ago - 1 comment
Labels: help wanted

#104 - Error in buildGraph with space = "genes"

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

#103 - add fixes for updatePairs, and Seurat variance scaling

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

#101 - Seurat version recommended

Issue - State: closed - Opened by yasodha30 over 3 years ago - 7 comments

#100 - about batch correction

Issue - State: closed - Opened by tanasa almost 4 years ago - 2 comments

#98 - Seurat compatibility feature requests

Issue - State: open - Opened by akramdi about 4 years ago - 3 comments
Labels: help wanted

#97 - About gene expression plots and gene signatures

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

#96 - Unable to view genewise expression from Seurat preprocessing

Issue - State: closed - Opened by mthimma about 4 years ago - 10 comments

#95 - Obtain feature loadings for pseudo-pca to input on monocle 3 for module analysis?

Issue - State: open - Opened by KrGurashi about 4 years ago - 3 comments
Labels: help wanted

#94 - Error installing Conos

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

#93 - Update documentation, dev

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

#92 - Interpretation of uncertainty in label propagation?

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

#91 - Add parameter `raster.dpi` in `con$plotEmbedding()`

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

#90 - remove dendrogram functions

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

#89 - Bugfix: add check if el is empty

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

#88 - Replacement error in buildGraph

Issue - State: closed - Opened by lazappi over 4 years ago - 8 comments

#87 - Error in installing Conos

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

#85 - changes to getPerCellTypeDE

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

#84 - source code should use TRUE/FALSE

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

#83 - Update ComplexHeatmap version

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

#82 - add note to README

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

#81 - Failed to install 'conos' from GitHub with Windows

Issue - State: closed - Opened by Lukadon77 over 4 years ago - 3 comments

#80 - Add wiki URL to README, Mac OS installation

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

#79 - Licensing

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

#78 - Convert std::cout to Rcpp::Rcout

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

#77 - bugfix: getPerCellTypeDE errors and NAs

Pull Request - State: closed - Opened by evanbiederstedt over 4 years ago - 7 comments

#76 - Write HDF5 for saveConosForScanPy()

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

#75 - Allow name access to multiple embeddings in conclass

Pull Request - State: closed - Opened by evanbiederstedt over 4 years ago - 18 comments

#74 - feature: update DESCRIPTION to use kharchenkolab/sccore

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

#73 - R6 documentation

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

#72 - use parseCellGroups in plotClusterBarplots

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

#71 - remove neighborhood averaging

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

#70 - Revise vignettes, fix papply() bugs in dev

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

#69 - removed getCorrectionVector, updated documentation

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

#68 - running CONOS on R-4.0.2

Issue - State: closed - Opened by tanasa over 4 years ago - 10 comments

#67 - Feature/readme revisions

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

#66 - Finding cluster marker genes

Issue - State: closed - Opened by sroyyors over 4 years ago - 5 comments

#65 - Minor fix on paragraph 150

Pull Request - State: closed - Opened by kant over 4 years ago

#64 - added install_name_tool conditional in src/Makevars

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

#62 - Allow to store multiple embeddings in the Conos object

Issue - State: closed - Opened by VPetukhov almost 5 years ago - 2 comments

#61 - Cell to sample mapping

Issue - State: closed - Opened by imranfanaswala almost 5 years ago - 2 comments

#60 - Document all conos methods in R6 class

Issue - State: closed - Opened by VPetukhov almost 5 years ago - 1 comment

#59 - Plotting gene with NA counts produces error

Issue - State: closed - Opened by rrydbirk almost 5 years ago - 4 comments

#58 - propagate_labels()

Issue - State: closed - Opened by mea2712 about 5 years ago

#56 - Unable to install on Mac due to -fopenmp

Issue - State: closed - Opened by JenniferWUSTL about 5 years ago - 12 comments

#55 - analysis of multiple time points * 2 replicates of scRNA-seq

Issue - State: closed - Opened by tanasa about 5 years ago - 3 comments

#54 - DE Between Sample Groups if no replicate is available

Issue - State: closed - Opened by bony45 about 5 years ago - 1 comment
Labels: question

#53 - error with single cell summary object

Issue - State: closed - Opened by bony45 about 5 years ago - 5 comments

#52 - embedGraph() as UMAP, output is LargeVis

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

#51 - 'test.stability' produces error in findCommunities

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

#50 - Reduce in con$plotPanel lost the original cell groups

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

#49 - Plotting gene with counts==0 and plot.na=F, all cells are red

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

#48 - Replace all checks for `groups` parameter with `parseCellGroups`

Issue - State: closed - Opened by VPetukhov over 5 years ago - 1 comment
Labels: refactor

#47 - Implement saving all files for ScanPy into a one HDF5 file instead

Issue - State: closed - Opened by GMaciag over 5 years ago
Labels: enhancement

#46 - Implement better coloring of adjacent clusters on large embeddings

Issue - State: closed - Opened by VPetukhov over 5 years ago - 2 comments
Labels: enhancement, help wanted

#45 - Better scanpy integration

Pull Request - State: closed - Opened by GMaciag over 5 years ago - 1 comment

#44 - RNA velocity integration

Pull Request - State: closed - Opened by GMaciag over 5 years ago - 3 comments

#43 - plotPanel(use.common.embedding=T) should fix the xlim/ylim values

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

#42 - getPerCellTypeDE errors in DESeq2

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

#41 - Is current implementation of getCorrectionVector correct?

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

#40 - Added findSubcommunities function

Pull Request - State: closed - Opened by rrydbirk over 5 years ago - 2 comments

#30 - Scanpy integration fails during analysis for scanpy > 1.4.1

Issue - State: closed - Opened by GMaciag over 5 years ago - 11 comments

#27 - can't get correctGenes

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

#23 - Aligning Count and TPM matrices

Issue - State: closed - Opened by ACastanza almost 6 years ago - 1 comment

#21 - Long runtime in buildGraph with score.component.variance=T

Issue - State: closed - Opened by rrydbirk almost 6 years ago - 5 comments