Skip to content

Issues: kharchenkolab/numbat

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clear current search query, filters, and sorts
63 Open 120 Closed
63 Open 120 Closed
Author
Filter by author
Loading
Label
Filter by label
Loading
Use alt + click/return to exclude labels
or ⇧ + click/return for logical OR
Projects
Filter by project
Loading
Milestones
Filter by milestone
Loading
Assignee
Filter by who’s assigned
Sort
Sort by
Newest Oldest Most commented Least commented Recently updated Least recently updated Best match
Most reactions
👍 👎 😄 🎉 😕 ❤️ 🚀 👀

Issues list

Cell Ranger Count Default Intronic Counting Impact
#155 by DarioS was closed Jan 21, 2024
1
Overwrite identifiers
#156 by SollyBunny was closed Jan 18, 2024
1
Error in find_common_diploid(bulks, gamma = gamma, alpha = alpha, ncores = ncores) : Error in smooth_segs(., min_genes = min_genes) :
#163 by whitneyt1 was closed Apr 5, 2024
6
Error in mutate(): ℹ In argument: snp_index = 1:n(). Caused by error: ! snp_index must be size 0 or 1, not 2.
#167 by cathalgking was closed Apr 5, 2024
8
How to generate the plotEmbedding in a numbat object?
#168 by christophechu was closed May 3, 2024
1
Running numbat in multiple samples from same patient
#176 by ccruizm was closed Apr 15, 2024
1
Error in mutate(., state = run_allele_hmm ... Not a matrix
#177 by whitneyt1 was closed Apr 5, 2024
2
n_states is 0 for CNV region with multiallelic CNVs are not called fixed Fixed in upcoming version
#178 by teng-gao was closed Sep 21, 2024
@teng-gao
Better error handling when one of the pileup fails
#179 by teng-gao was closed Mar 21, 2024
bulk_clones plot "CNV state" legend colors fixed Fixed in upcoming version
#182 by igordot was closed Sep 21, 2024
7
Excluding segs_loh causes multiple CNV states for the same segment tofix
#183 by teng-gao was closed May 3, 2024
2
Input only the gene expression matrix
#187 by Mashuaiii was closed Apr 28, 2024
2
Numbat assigned clone coloring in Panel.png
#191 by quail768 was closed May 30, 2024
reorder cell order in heatmap output
#192 by patelgrp was closed Jun 4, 2024
2
plot_phylo_heatmap() does not work
#195 by kobolock was closed Jul 18, 2024
1
run_numbat() with multiple samples
#196 by kobolock was closed Jul 22, 2024
1
Mouse genetic background - Both parental strains are reference C57
#198 by radiasso was closed Jul 22, 2024
1
(hom_rate > 0.4) {: missing value where TRUE/FALSE needed
#200 by stela2502 was closed Aug 12, 2024
converting existing FACETS CNV calls from WGS to Numbat format for input to "segs_consensus_fix"
#201 by ahwanpandey was closed Sep 5, 2024
1
The difference between cnv_state and cnv_state_map in joint_post result file
#204 by Mashuaiii was closed Sep 5, 2024
1
ProTip! Find all open issues with in progress development work with linked:pr.