Ecosyste.ms: Issues

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

GitHub / hemberg-lab/sc3 issues and pull requests

#111 - Question about <NA> labels from cell clustering via SC3

Issue - State: closed - Opened by yxy92 10 months ago - 1 comment

#110 - sc3_run_svm has a prediction issue

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

#109 - Running SC3 in integrated data

Issue - State: closed - Opened by anemartinezlarrinaga2898 almost 2 years ago - 1 comment

#108 - could not find function "calculate_distance"

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

#107 - long vectors are not supported in .C

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

#107 - long vectors are not supported in .C

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

#106 - Saving SC3 clustering output as csv files

Issue - State: closed - Opened by bsamal20 almost 3 years ago - 3 comments

#106 - Saving SC3 clustering output as csv files

Issue - State: closed - Opened by bsamal20 almost 3 years ago - 3 comments

#105 - saving SC3 output

Issue - State: open - Opened by bsamal20 almost 3 years ago

#104 - rewritten parallelism to BiocParallel package

Pull Request - State: open - Opened by gorgitko over 3 years ago - 6 comments

#103 - one node produced an error: Error in ED2(data)

Issue - State: open - Opened by eshraaqsaeed over 3 years ago - 1 comment

#103 - one node produced an error: Error in ED2(data)

Issue - State: open - Opened by eshraaqsaeed over 3 years ago - 1 comment

#101 - Error in rowSums(out_pathway) : 'x' must be an array of at least two dimensions

Issue - State: closed - Opened by zina-R about 4 years ago - 1 comment

#101 - Error in rowSums(out_pathway) : 'x' must be an array of at least two dimensions

Issue - State: closed - Opened by zina-R about 4 years ago - 1 comment

#99 - Which remove-batch-effect package work best with SC3?

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

#98 - Sparse matrix causes errors

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

#98 - Sparse matrix causes errors

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

#97 - Error in prcomp.default

Issue - State: closed - Opened by dsimps1993 about 5 years ago - 4 comments

#95 - Gene names lost after get_marker_genes()

Issue - State: open - Opened by friedue over 5 years ago

#95 - Gene names lost after get_marker_genes()

Issue - State: open - Opened by friedue over 5 years ago

#94 - Plot expression on given list of genes

Issue - State: closed - Opened by shabs24 over 5 years ago - 1 comment

#94 - Plot expression on given list of genes

Issue - State: closed - Opened by shabs24 over 5 years ago - 1 comment

#93 - Clustering for more than 10000 Genes

Issue - State: closed - Opened by hkarakurt8742 over 5 years ago - 3 comments

#93 - Clustering for more than 10000 Genes

Issue - State: closed - Opened by hkarakurt8742 over 5 years ago - 3 comments

#92 - SC3 with Batch Correction

Issue - State: closed - Opened by hkarakurt8742 over 5 years ago - 1 comment

#92 - SC3 with Batch Correction

Issue - State: closed - Opened by hkarakurt8742 over 5 years ago - 1 comment

#91 - How to calculate D?

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

#91 - How to calculate D?

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

#90 - Copy transformations to @reducedDims when possible

Pull Request - State: closed - Opened by nh3 over 5 years ago

#90 - Copy transformations to @reducedDims when possible

Pull Request - State: closed - Opened by nh3 over 5 years ago

#89 - Fixed the sparse matrix issue

Pull Request - State: open - Opened by zhangguy over 5 years ago - 1 comment

#89 - Fixed the sparse matrix issue

Pull Request - State: open - Opened by zhangguy over 5 years ago - 1 comment

#88 - error running sc3_plot_de_genes

Issue - State: open - Opened by qiaowei-vvjoe over 5 years ago - 8 comments

#88 - error running sc3_plot_de_genes

Issue - State: open - Opened by qiaowei-vvjoe over 5 years ago - 8 comments

#87 - No gene names in export results

Issue - State: open - Opened by dsimps1993 almost 6 years ago - 4 comments

#87 - No gene names in export results

Issue - State: open - Opened by dsimps1993 almost 6 years ago - 4 comments

#86 - SC3 error on linux server: Not compatible with requested type

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

#86 - SC3 error on linux server: Not compatible with requested type

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

#85 - Which data type for clustering

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

#85 - Which data type for clustering

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

#84 - sc3_plot_de_genes and sc3_plot_markers problems

Issue - State: closed - Opened by Santos22903 about 6 years ago - 2 comments

#84 - sc3_plot_de_genes and sc3_plot_markers problems

Issue - State: closed - Opened by Santos22903 about 6 years ago - 2 comments

#83 - Consider using Forks for parallelism?

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

#83 - Consider using Forks for parallelism?

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

#82 - is it possible to surpress the message in `sc3` function.

Issue - State: open - Opened by LuyiTian about 6 years ago - 1 comment

#82 - is it possible to surpress the message in `sc3` function.

Issue - State: open - Opened by LuyiTian about 6 years ago - 1 comment

#81 - #UMI counts table

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

#80 - Small suggestion for sc3_prepare() documentation

Issue - State: open - Opened by PeteHaitch about 6 years ago - 1 comment
Labels: enhancement

#80 - Small suggestion for sc3_prepare() documentation

Issue - State: open - Opened by PeteHaitch about 6 years ago - 1 comment
Labels: enhancement

#79 - Plot column names

Issue - State: open - Opened by simone-rizzetto about 6 years ago - 1 comment
Labels: enhancement

#79 - Plot column names

Issue - State: open - Opened by simone-rizzetto about 6 years ago - 1 comment
Labels: enhancement

#78 - Specify custom genes/features

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

#78 - Specify custom genes/features

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

#77 - Clusters for max 5000 cells

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

#77 - Clusters for max 5000 cells

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

#76 - SC3 repeatedly loads packages while running and has data display issues

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

#76 - SC3 repeatedly loads packages while running and has data display issues

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

#75 - Not clear how SC3 exactly works

Issue - State: closed - Opened by CodeInTheSkies over 6 years ago - 5 comments

#75 - Not clear how SC3 exactly works

Issue - State: closed - Opened by CodeInTheSkies over 6 years ago - 5 comments

#73 - Error in `[.default`(clusts, , paste0("sc3_", hash.table[i, 1], "_clusters"))

Issue - State: open - Opened by DrLucyMac over 6 years ago - 10 comments

#72 - Error in checkForRemoteErrors(val) :

Issue - State: closed - Opened by 15084921898 over 6 years ago - 2 comments

#72 - Error in checkForRemoteErrors(val) :

Issue - State: closed - Opened by 15084921898 over 6 years ago - 2 comments

#71 - Excluding principal components from clustering

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

#71 - Excluding principal components from clustering

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

#70 - Annotation colour palette in heatmaps

Issue - State: open - Opened by wikiselev over 6 years ago
Labels: enhancement

#70 - Annotation colour palette in heatmaps

Issue - State: open - Opened by wikiselev over 6 years ago
Labels: enhancement

#69 - Pass k_estimate results if ks is NULL; fixes #67

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

#69 - Pass k_estimate results if ks is NULL; fixes #67

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

#68 - Large number of NA's when run on large dataset.

Issue - State: closed - Opened by TChan92 over 6 years ago - 17 comments

#68 - Large number of NA's when run on large dataset.

Issue - State: closed - Opened by TChan92 over 6 years ago - 17 comments

#67 - k_estimator output not passed to sc3 wrapper function

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

#67 - k_estimator output not passed to sc3 wrapper function

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

#66 - Feature request: option to specify assay used

Issue - State: closed - Opened by dkoppstein over 6 years ago - 5 comments

#66 - Feature request: option to specify assay used

Issue - State: closed - Opened by dkoppstein over 6 years ago - 5 comments

#64 - Error in ED2(data)

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

#64 - Error in ED2(data)

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

#63 - default for `n_cores`

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

#63 - default for `n_cores`

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

#62 - export plot from SC3

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

#62 - export plot from SC3

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

#60 - Is there a way to pull out the stability index matrix from the SC3 object?

Issue - State: open - Opened by yingzhang121 almost 7 years ago - 7 comments
Labels: enhancement

#60 - Is there a way to pull out the stability index matrix from the SC3 object?

Issue - State: open - Opened by yingzhang121 almost 7 years ago - 7 comments
Labels: enhancement

#59 - Error in !isSpike(object) : invalid argument type

Issue - State: open - Opened by yicheinchang almost 7 years ago - 3 comments
Labels: enhancement

#59 - Error in !isSpike(object) : invalid argument type

Issue - State: open - Opened by yicheinchang almost 7 years ago - 3 comments
Labels: enhancement

#58 - Update calculate_stability.Rd

Pull Request - State: closed - Opened by tallulandrews almost 7 years ago - 1 comment

#58 - Update calculate_stability.Rd

Pull Request - State: closed - Opened by tallulandrews almost 7 years ago - 1 comment

#57 - Remove one N from the denominator of stability

Pull Request - State: closed - Opened by tallulandrews almost 7 years ago - 2 comments

#57 - Remove one N from the denominator of stability

Pull Request - State: closed - Opened by tallulandrews almost 7 years ago - 2 comments

#56 - Performance Enhancements, Laplacian matrix improvements

Pull Request - State: closed - Opened by pati-ni almost 7 years ago