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replies
286
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How to format "I" and "D" in vcf version 4.2 for liftover analysis in GATK
gatk vcf liftover
updated 7 days ago by 43k • written 7 days ago by ▴ 260
0
votes
0
replies
127
views
Xenium multi sample data
batch annotation cell Xenium effect
9 days ago by Omics data mining ▴ 260
0
votes
0
replies
419
views
cnetplot enrichment graph to cytoscape
clusterprofiler cnetplot enrichplot
11 months ago by Omics data mining ▴ 260
0
votes
0
replies
1.6k
views
from seurat to scanpy data conversion and re-scaling
transctiptome eurat scanpy conversion spatial
12 months ago by Omics data mining ▴ 260
1
vote
1
reply
994
views
Right assay and slot for the extraction of normalized data after "sct normalization" and "anchor based integration"
single normalization integration cell sct anchor seurat based
updated 12 months ago by ★ 1.8k • written 12 months ago by ▴ 260
0
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1
reply
486
views
pipeline for correlation of RNASeq and Methylation data
rnaseq methylation correlation normalization data
updated 13 months ago by ★ 2.9k • written 13 months ago by ▴ 260
0
votes
1
reply
599
views
Customizable pvalue scales in clusterprofiler
clusterprofiler
updated 13 months ago by 13k • written 13 months ago by ▴ 260
2
votes
2
replies
909
views
clusterprofiler dotplot facet_grid plot based on ONTOLOGY
dotplot clusterprofiler facet_grid
13 months ago by Omics data mining ▴ 260
0
votes
0
replies
342
views
normalization and integration of two independent single cell cohorts
single-cell batch-effect normalization
updated 13 months ago by 43k • written 13 months ago by ▴ 260
0
votes
1
reply
1.2k
views
normalized score for SpatialFeaturePlot
Spatial Transcriptome normalization integration Seurat
updated 14 months ago by ★ 1.8k • written 14 months ago by ▴ 260
1
vote
2
replies
663
views
Visualization of Enrichment score for spatial 10x visium samples
visium transctiptome 10x enrichment scores spatial
15 months ago by Omics data mining ▴ 260
1
vote
2
replies
652
views
deconvolution of spatial transcriptome
deconvolution spatial transcriptome
updated 15 months ago by ★ 3.9k • written 15 months ago by ▴ 260
0
votes
1
reply
1.8k
views
change color and scale in SpatialFeaturePlot
clustering Seurat spatial-transcriptome
updated 16 months ago by 43k • written 16 months ago by ▴ 260
0
votes
0
replies
991
views
error plotting spatial data in scanpy
scanpy spatial-transcriptome
updated 16 months ago by 43k • written 16 months ago by ▴ 260
2
votes
0
replies
550
views
Input at BINDetect step (for TOBIAS pipeline) with multiple files
differential ATAC-Seq tobias motifs
16 months ago by Omics data mining ▴ 260
1
vote
6
replies
3.3k
views
error in pipeline installation dependent on numpy version 1.18.5
cnn numpy imaging python
16 months ago by Omics data mining ▴ 260
3
votes
8
replies
6.4k
views
bait interval list for picard collecthsmetrices
picard alignment exome
13 months ago by Omics data mining ▴ 260
1
vote
1
reply
521
views
DESeq2 with multiple conditional data
multi differential DESeq2 genes factor
updated 17 months ago by 13k • written 17 months ago by ▴ 260
8
votes
6
replies
3.3k
views
How to include spatial coordinate data into anndata within scanpy
scanpy visium transcriptome spatial 10X
updated 4 months ago by • 0 • written 19 months ago by ▴ 260
1
vote
1
reply
521
views
Batch effect of sequencing data that were sequenced in different locations
effect batch DESeq2
updated 19 months ago by 82k • written 19 months ago by ▴ 260
0
votes
0
replies
435
views
Error plotting the markers in sc.pl.rank_genes_groups_dotplot
scanpy trasncriptome seurat spatial
19 months ago by Omics data mining ▴ 260
0
votes
1
reply
489
views
identification of overlapped, proximal and distal gene for peak regions
chip idenfication peak seq gene
updated 19 months ago by ▴ 410 • written 19 months ago by ▴ 260
1
vote
2
replies
577
views
cluster identification and DEGs in single cell data
deg cluster seurat analysis
20 months ago by Omics data mining ▴ 260
3
votes
6
replies
1.1k
views
nested elements in bed file using awk
coordinates bedops genome awk
19 months ago by Omics data mining ▴ 260
4
votes
1
reply
1.1k
views
SCTransform in single cell
SCTransform seurat
updated 20 months ago by 142k • written 20 months ago by ▴ 260
1
vote
4
replies
644
views
overlap statistics among multiple bed files
bedtools
updated 11 months ago by 43k • written 20 months ago by ▴ 260
0
votes
2
replies
506
views
exportFASTA not working
exportFASTA biomart getSeq
20 months ago by Omics data mining ▴ 260
0
votes
2
replies
536
views
Filteration of uniquely mapped reads
samtools bam
updated 11 months ago by 43k • written 20 months ago by ▴ 260
0
votes
4
replies
1.7k
views
conda env in snakemake
snakemake conda
20 months ago by Omics data mining ▴ 260
0
votes
1
reply
2.9k
views
SCTransform + Harmony in Seurat for batch correction
batch transcriptome spatial correction Seurat
updated 24 months ago by ▴ 10 • written 2.2 years ago by ▴ 260
0
votes
0
replies
408
views
calculate the variance across the samples
10X spatial cell single visium
2.2 years ago by Omics data mining ▴ 260
0
votes
2
replies
575
views
from dexseq results to alternative splicing events identification
dexseq alternative splicing
2.2 years ago by Omics data mining ▴ 260
0
votes
2
replies
849
views
Differential transcript usage from Salmon data
DTU rnaseqDTU transcript differential stageR
updated 16 months ago by ▴ 120 • written 2.2 years ago by ▴ 260
2
votes
3
replies
988
views
inter and intra-sample variance in 10X visium spatial transcriptome data
transcriptome cell single spatial
updated 20 months ago by 142k • written 2.2 years ago by ▴ 260
0
votes
5
replies
1.2k
views
unmapped reads from 10X visium spaceranger bam file
transcriptome 10X spatial visium
updated 2.2 years ago by 161k • written 2.2 years ago by ▴ 260
6
votes
4
replies
1.7k
views
gene set enrichment in clusterprofiler
clusterprofiler gene enrichment analysis set
updated 2.2 years ago by ▴ 20 • written 2.3 years ago by ▴ 260
0
votes
2
replies
1.5k
views
gseGO for multiple groups
clusterProfiler gseKEGG gseGO
2.3 years ago by Omics data mining ▴ 260
1
vote
2
replies
1.3k
views
Upset plot in ComplexHeatmap
ComplexHeatmap Upsetplot
updated 2.3 years ago by ★ 16k • written 2.3 years ago by ▴ 260
0
votes
1
reply
860
views
impulseDE2 input
normalized count input raw impulseDE2
updated 2.4 years ago by ▴ 200 • written 2.4 years ago by ▴ 260
0
votes
3
replies
1.1k
views
spatial 10X visum analysis
spatial 10X visium
updated 2.4 years ago by 13k • written 2.4 years ago by ▴ 260
0
votes
2
replies
7.5k
views
conversion of ensembl to gene_symbol in seurat
Seurat conversion spatial transcriptome
2.4 years ago by Omics data mining ▴ 260
2
votes
4
replies
1.9k
views
UMI extraction from 10X visium spatial transcriptome data
umi_tools UMI spatial-transcriptome
updated 11 months ago by 43k • written 2.4 years ago by ▴ 260
0
votes
0
replies
520
views
Patient-to-patient similarities network
SNFtools multi omics
3.3 years ago by Omics data mining ▴ 260
0
votes
0
replies
575
views
Error running gene expression based ProTINA
ProTINA Time-Series gene-expression
updated 11 months ago by 43k • written 3.5 years ago by ▴ 260
0
votes
2
replies
985
views
Selection of SNPs after imputation
gwas imputation
updated 3.8 years ago by ▴ 140 • written 3.8 years ago by ▴ 260
0
votes
0
replies
1.1k
views
GetPileupSummaries for each chromosome
GATK
3.8 years ago by Omics data mining ▴ 260
1
vote
3
replies
1.2k
views
minimum reads for the splicing event analysis ?
alternative splicing isoform expression
updated 3.9 years ago by 15k • written 3.9 years ago by ▴ 260
0
votes
0
replies
686
views
include vcf header
varscan
4.3 years ago by Omics data mining ▴ 260
1
vote
0
replies
955
views
TCGA data , filtration and normalization
genomics omics TCGA normalization
4.3 years ago by Omics data mining ▴ 260
2
votes
6
replies
4.2k
views
error while running vcf2maf
vcf2maf SNP rnaseq
updated 4.4 years ago by ▴ 180 • written 5.8 years ago by ▴ 260
91 results • Page 1 of 2
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