akdess CaSpER issues - Githubissues

akdess / CaSpER

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Why did you use control sample ids in loh for BRCA and GBM data, not use in Meningioma dataset?

#87 kadersaribulak opened 4 days ago
0
Error in plotBAFInSeperatePages and plotSingleCellLargeScaleEventHeatmap

#86 mehlu22 opened 1 month ago
0
Error in running Casper

#85 mehlu22 opened 1 month ago
0
Batch correction for raw scRNAseq from multiple patients

#84 danyangli123 opened 2 months ago
0
phylogenetic tree/tumor subclone

#83 Mashuaiii opened 8 months ago
0
how to create geno.rna object in https://rpubs.com/akdes/673120

#82 BioAmelie opened 9 months ago
2
Using CaSpER with single bulk RNA-Seq sample

#81 hkarakurt8742 opened 11 months ago
2
CNV score

#80 alkurowska opened 1 year ago
0
Excluding/keeping reads from normal cells in the bam for BAFExtract

#79 kzb193 opened 1 year ago
0
runCaSpER error

#78 baoyl818 opened 2 years ago
2
plotHeatmap function can only show cell ids instead of patient ids (group names)

#77 lifan18 opened 2 years ago
1
outputs from bulk sequencing

#76 pirlowang opened 2 years ago
0
single-cell dataset (not 10x) running issue with genome version hg38

#75 lifan18 closed 2 years ago
5
Will there be an update to support mm10?

#74 thestarocean opened 2 years ago
0
Missing dropbox link for genome_list and genome_fasta_pileup_dir files

#73 ahdee closed 2 years ago
0
runCaSpER error

#72 SaritaPoonia opened 2 years ago
1
Negative TPR in calcROC() calcultation

#71 Fabian-RY opened 2 years ago
0
runCaSpER Error

#70 shalbahl opened 2 years ago
0
how to prepare the BAF file for single cell data

#69 xinmiaoyan opened 2 years ago
0
runCaSpER : Error in value[[jvseq[[jjj]]]] : subscript out of bounds

#68 nmc-ei closed 3 years ago
3
Non model species using casper

#67 reuvenieli00 opened 3 years ago
3
generateAnnotation returning curl error

#66 Lakshya3141 opened 3 years ago
2
regarding object creation

#65 guttula91 opened 3 years ago
0
Running CaSpER without Recerence Normal samples?

#64 lmasatti opened 3 years ago
3
Annotation file for hg38

#63 Troyee13 closed 3 years ago
2
error of loh <- readBAFExtractOutput

#62 deb0612 opened 3 years ago
7
Does CaSpER adaptable to small sample size such as 10 cells?

#61 wangteng0605 opened 3 years ago
0
memory issue with runCaSpER(): cannot allocate vector of size...

#60 marlaherr closed 3 years ago
0
How can we get more stringent CNV calls?

#59 AidenSb opened 3 years ago
0
Error in if (abs(loglik[i] - loglik[i - 1]) < 0.1 || loglik[i] < loglik[i - : missing values where TRUE/FALSE values are required

#58 wqy399 opened 3 years ago
4
Identification of Tumor and Non Tumor cells

#57 singlecellCRC-hub opened 3 years ago
0
"forward_backward" not available for .Call() for package "CaSpER"

#56 amcruise opened 3 years ago
1
I obtained different results with Yale Meningioma dataset

#55 lmalet opened 3 years ago
1
Control cells also analyzed for CNVs?

#54 rhlgyb opened 3 years ago
3
is CaSpER limited by the type of sequencing protocol ?

#53 moutazhelal opened 3 years ago
0
Problem with runCaSpER

#52 lmalet closed 3 years ago
1
selecting normal cell clusters in 10X single cell tutorial

#51 cstubben opened 3 years ago
1
Minimum mapping quality threshold for STAR-aligned BAM file

#50 arjun0502 closed 3 years ago
0
Subset a region or chromosome from CaSpER object

#49 abedkurdi closed 3 years ago
1
Error when using readBAFExtractOutput

#48 moutazhelal closed 3 years ago
2
Add biocViews keyword to DESCRIPTION

#47 grst closed 3 years ago
1
plotHeatmap() saves the plot in the working directory and not at the specified path

#46 ftucos closed 3 years ago
3
Which OS was Casper developed for?

#45 nmc-ei closed 3 years ago
0
CaSpER for bulk RNA-seq data

#44 dreammxy opened 3 years ago
2
HMM Segmentation Error "memory not mapped"

#43 chatterjee89 opened 3 years ago
3
workflow for merging multiple scRNA samples

#42 hartlama opened 3 years ago
1
BAFExtract could not find 1_allele_counts.bin.gz.

#41 nmc-ei closed 3 years ago
0
Control sample for scRNAseq data

#40 laillern opened 3 years ago
1
generating genoMat

#39 garci1294 closed 3 years ago
2
fix plotHeatmap() ignoring filename parameter

#38 ftucos closed 3 years ago
1