Ecosyste.ms: Issues

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GitHub / reactome/ReactomeGSA issues and pull requests

#89 - Timeout was reached: [gsa.reactome.org] SSL/TLS connection timeout

Issue - State: open - Opened by cdkodira 18 days ago - 1 comment

#88 - 87 ribo seq

Pull Request - State: open - Opened by Gionmattia about 2 months ago

#87 - R Client for Ribo Seq data

Issue - State: open - Opened by alexgrent about 2 months ago

#82 - 81 pseudo bulk

Pull Request - State: open - Opened by alexgrent 4 months ago - 10 comments

#81 - Add scRNA seq using pseudo bulk

Issue - State: open - Opened by alexgrent 4 months ago

#80 - Prepare for upcoming Seurat v5 release

Issue - State: open - Opened by Gesmira about 1 year ago

#79 - ssGSEA FDR?

Issue - State: open - Opened by domi84 about 1 year ago - 3 comments

#78 - plot_gsva_pathway label squished and how to assign specific color

Issue - State: open - Opened by camilla0801 over 1 year ago - 1 comment

#77 - How can I save the heatmap from `plot_gsva_heatmap` with `ggplot2` ?

Issue - State: closed - Opened by camilla0801 over 1 year ago - 2 comments
Labels: question

#76 - convert_reactome_result function not found

Issue - State: closed - Opened by nearvh over 1 year ago - 1 comment

#75 - ReactomeGSA API not working?

Issue - State: closed - Opened by quyaingo over 1 year ago - 6 comments

#74 - Obtaining features from `perform_reactome_analysis` function

Issue - State: closed - Opened by ejc043 over 1 year ago - 3 comments

#73 - Create function for cluster-level pathway enrichment for scRNA-seq data

Issue - State: open - Opened by jgriss over 1 year ago
Labels: enhancement

#72 - Statistical significance from single-cell cluster analysis

Issue - State: closed - Opened by LuciaJim over 1 year ago - 6 comments

#71 - Pathway analysis on Spatial data 10x Visium

Issue - State: closed - Opened by cathalgking almost 2 years ago - 3 comments
Labels: question

#69 - Lazy database

Issue - State: closed - Opened by querques almost 2 years ago - 1 comment
Labels: invalid

#67 - Add support for group-wise comparison of scRNA-seq data

Issue - State: open - Opened by jgriss about 2 years ago
Labels: enhancement

#66 - perform_reactome_analysis does'nt create a reactome visualization

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

#65 - use the latest Reactome release

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

#64 - Potential bug: Ensure that groups can also be integers

Issue - State: open - Opened by jgriss over 2 years ago
Labels: bug

#63 - Selected Pathways

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

#59 - Convert http to https in report download urls

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

#58 - Request failed (503 - Service Unavailable)

Issue - State: closed - Opened by Luq16 almost 3 years ago - 1 comment

#55 - the API of gsa.reactome not work for analyse_sc_clusters

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

#54 - Use consistent FDR thresholds to define significantly regulated pathways

Issue - State: closed - Opened by jgriss almost 3 years ago - 1 comment
Labels: bug, enhancement

#53 - Add number of mapped genes in GSVA results

Issue - State: open - Opened by jgriss about 3 years ago
Labels: enhancement

#48 - pathway hierarchy for annotating pathways

Issue - State: open - Opened by bravedu01 about 3 years ago - 3 comments
Labels: enhancement

#47 - The plot_gsva_heatmap function make a wrong plot with a reversed trend.

Issue - State: closed - Opened by bravedu01 about 3 years ago - 3 comments
Labels: invalid

#46 - Error in plot_gsva_pca(gsva_pbmc) : object 'gsva_result' not found

Issue - State: closed - Opened by bravedu01 about 3 years ago - 8 comments
Labels: bug

#45 - Request failed (503 - Service Unavailable): Failed to connect to storage system

Issue - State: closed - Opened by Ankita-1211 about 3 years ago - 5 comments

#44 - Error: Failed to connect to ReactomeGSA

Issue - State: closed - Opened by Ankita-1211 about 3 years ago - 2 comments

#43 - Check that passed metadata fits expression values in add_dataset

Issue - State: open - Opened by jgriss about 3 years ago
Labels: enhancement

#38 - Request Failed -- 503 -- Service Unavailable -- Is Reactome API down?

Issue - State: closed - Opened by hcchau418 about 3 years ago - 2 comments
Labels: bug

#36 - Running reactomeGSA for species other than human

Issue - State: closed - Opened by Ankita-1211 about 3 years ago
Labels: question

#34 - Error: Only one identification found: 'RNA_snn_res.0.6

Issue - State: closed - Opened by Ankita-1211 about 3 years ago - 1 comment
Labels: question

#32 - heatmap labels of the cells clusters are squished

Issue - State: closed - Opened by jjyotikataria over 3 years ago

#28 - reproducibility of the ReactomeGSA

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

#27 - Error: Failed to connect to ReactomeGSA

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

#26 - Not getting cluster names in the dataframe after pathway expression

Issue - State: closed - Opened by jjyotikataria over 3 years ago - 1 comment
Labels: question

#25 - where to find start_reactome_analysis?

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

#24 - scRNA-seq pathway scoring per condition

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

#23 - Make mapping results (entities per pathway) available in R

Issue - State: open - Opened by jgriss over 3 years ago
Labels: enhancement

#22 - How to automatically download table displayed in reactome link

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

#21 - Error at too many cells – Cholmod error 'problem too large'

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

#20 - Typo in tutorial

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

#19 - How to label the points on the graph itself using plot_gsva_pca()?

Issue - State: closed - Opened by levinhein over 3 years ago - 1 comment
Labels: help wanted

#18 - Error with curl HTTP access

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

#17 - analyse_sc_clusters with the "Error in readBin(3L, raw(0), 32768L) : "

Issue - State: closed - Opened by Charlesyip2016 over 3 years ago - 1 comment

#16 - An error when using analyse_sc_clusters

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

#15 - Label clusters using plot_gsva_pca

Issue - State: closed - Opened by rpauly almost 4 years ago - 1 comment
Labels: question

#13 - analyse_sc_clusters() not found

Issue - State: closed - Opened by aditisk almost 4 years ago - 4 comments
Labels: question

#13 - analyse_sc_clusters() not found

Issue - State: closed - Opened by aditisk almost 4 years ago - 4 comments
Labels: question

#12 - Add `group.by` parameter to `analyse_sc_clusters`

Issue - State: open - Opened by jgriss about 4 years ago
Labels: enhancement

#11 - How do you validate your results?

Issue - State: closed - Opened by Abelsufu over 4 years ago - 5 comments
Labels: question

#11 - How do you validate your results?

Issue - State: closed - Opened by Abelsufu over 4 years ago - 5 comments
Labels: question

#10 - Add support to directly analyse Seurat clusters

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

#9 - Add heatmap plot for GSVA results

Issue - State: closed - Opened by jgriss over 4 years ago - 1 comment
Labels: enhancement

#8 - Fix Reactome visualization for ssGSEA if size filter is applied

Issue - State: open - Opened by jgriss over 4 years ago
Labels: bug

#7 - Add signature for add_dataset supporting a matrix

Issue - State: open - Opened by jgriss over 4 years ago
Labels: enhancement

#6 - Add feature to get members of a specific pathway

Issue - State: open - Opened by jgriss over 4 years ago
Labels: enhancement

#5 - Add function to highlight specific pathways in plots

Issue - State: open - Opened by jgriss over 4 years ago
Labels: enhancement

#4 - Add support for long running analyses

Issue - State: open - Opened by jgriss over 4 years ago
Labels: enhancement

#3 - Add remove_dataset function

Issue - State: closed - Opened by jgriss over 5 years ago - 1 comment
Labels: enhancement

#2 - pathways function does not sort pathways

Issue - State: closed - Opened by jgriss over 5 years ago - 1 comment
Labels: bug

#1 - add_dataset with overwrite = TRUE can duplicate dataset

Issue - State: closed - Opened by jgriss over 5 years ago - 1 comment
Labels: bug