prabhakarlab/Banksy issues and pull requests

#41 - Error in RunBanksy code

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

#40 - Extracting Cells IDs that were used to generate Banksy K_geom neighborhood

Issue - State: closed - Opened by Alwash-317 4 months ago - 1 comment

#39 - Running Banksy on large Xenium Dataset

Issue - State: closed - Opened by Alwash-317 5 months ago - 2 comments

#38 - Error in RunBanksy with Visium HD data

Issue - State: closed - Opened by meaksu 6 months ago - 2 comments

#37 - link to the `center = TRUE` argument

Issue - State: closed - Opened by vipulsinghal02 6 months ago - 1 comment

#36 - Strange staggering behavior

Issue - State: closed - Opened by jwangbio 7 months ago - 5 comments

#35 - choose the right k_geom parameter

Issue - State: closed - Opened by rocketeer1998 8 months ago - 2 comments

#34 - RunBanksy function issue

Issue - State: closed - Opened by mvereten 8 months ago - 2 comments

#33 - Visium notes

Pull Request - State: closed - Opened by vipulsinghal02 8 months ago

#32 - RunBanksy error

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

#31 - Banksy on integrated samples creating sample-specific clusters

Issue - State: closed - Opened by rstagnit 9 months ago - 2 comments

#30 - prop_thres in smoothLabels

Issue - State: closed - Opened by cindyfang70 9 months ago - 2 comments

#29 - Typo in smoothLabels documentation example

Issue - State: closed - Opened by cindyfang70 9 months ago - 2 comments

#28 - Subclustering capability

Issue - State: closed - Opened by KoichiHashikawa 9 months ago - 8 comments

#27 - Running Banksy on Harmonized Seurat Object

Issue - State: closed - Opened by rstagnit 10 months ago - 5 comments

#26 - object 'compute.banksyMatrices' not found

Issue - State: closed - Opened by rstagnit 10 months ago - 4 comments

#25 - Multi sample analysis on seurat object

Issue - State: closed - Opened by alirezaah98 10 months ago - 2 comments

#24 - After loading the Banksy package, an error occurs when trying to create an object using BanksyObject.

Issue - State: closed - Opened by yuanjiao123 10 months ago - 2 comments

#23 - Double the features in BANKSY assay in seurat object

Issue - State: closed - Opened by alirezaah98 11 months ago - 1 comment

#22 - SCT instead of log transformed

Issue - State: closed - Opened by bmanzato 11 months ago - 1 comment

#21 - There is an M parameter in RunBanksy function in the analysis code but not in the manual.

Issue - State: closed - Opened by yuanjiao123 11 months ago - 1 comment

#20 - Error in `[.data.table`(knn_df, , abs(gcm[, to, drop = FALSE] %% (weight : negative length vectors are not allowed Calls: computeBanksy ... <Anonymous> -> computeHarmonics -> [ -> [.data.table

Issue - State: closed - Opened by WangGuixiangCoder 11 months ago - 3 comments

#19 - missing code in multi-sample vignette page

Issue - State: closed - Opened by abraham-abin13 11 months ago - 2 comments

#18 - Choose the right lambda for cell clustering and cell type annotation

Issue - State: closed - Opened by yiwang12 11 months ago - 3 comments

#17 - object compute.banksymatrics not found

Issue - State: closed - Opened by alirezaah98 11 months ago - 6 comments

#16 - Error in value[[3L]](cond) : Not enough neighbours at k_geom

Issue - State: closed - Opened by williamsdrake 12 months ago - 2 comments

#15 - Error: No images present in this Seurat object

Issue - State: closed - Opened by JLiLab 12 months ago - 10 comments

#14 - Question about normalization

Issue - State: closed - Opened by Jieran-S 12 months ago - 2 comments

#13 - R Version Issue

Issue - State: closed - Opened by calebhallinan about 1 year ago - 2 comments

#12 - Implements smoothing and parallelisation

Pull Request - State: closed - Opened by jleechung over 1 year ago

#11 - ClusterBanksy throws error: "REAL() can only be applied to a 'numeric', not a 'NULL'"

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

#10 - Implementation of azimuthal Gabor filters

Pull Request - State: closed - Opened by jleechung almost 2 years ago

#9 - some requests

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

#8 - About data preprocessing

Issue - State: closed - Opened by huoyuying over 2 years ago - 2 comments
Labels: question

#7 - Warning in `RunUMAP` with multiple lambdas and pca=FALSE

Issue - State: closed - Opened by retogerber almost 3 years ago - 2 comments

#6 - add the nbr matrix from bank object directly to the seurat object for subsequent analysis

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

#5 - Multi-sample integration analysis

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

#4 - Calculate the correlation of the expression of two genes

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

#3 - How to change a BanksyObject to seurat object ?

Issue - State: closed - Opened by hzongyao almost 3 years ago - 2 comments

#2 - Add examples and data blackout.

Pull Request - State: closed - Opened by jleechung almost 3 years ago

#1 - Update main

Pull Request - State: closed - Opened by jleechung almost 3 years ago

GitHub / prabhakarlab/Banksy issues and pull requests