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0
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407
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cnetplot enrichment graph to cytoscape
clusterprofiler cnetplot enrichplot
11 months ago by Omics data mining ▴ 260
0
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0
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1.6k
views
from seurat to scanpy data conversion and re-scaling
transctiptome eurat scanpy conversion spatial
11 months ago by Omics data mining ▴ 260
1
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1
reply
969
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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
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1
reply
477
views
pipeline for correlation of RNASeq and Methylation data
rnaseq methylation correlation normalization data
updated 12 months ago by ★ 2.9k • written 12 months ago by ▴ 260
0
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1
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579
views
Customizable pvalue scales in clusterprofiler
clusterprofiler
updated 12 months ago by 13k • written 12 months ago by ▴ 260
2
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2
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870
views
clusterprofiler dotplot facet_grid plot based on ONTOLOGY
dotplot clusterprofiler facet_grid
12 months ago by Omics data mining ▴ 260
0
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0
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336
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normalization and integration of two independent single cell cohorts
single-cell batch-effect normalization
updated 12 months ago by 43k • written 12 months ago by ▴ 260
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1
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1.1k
views
normalized score for SpatialFeaturePlot
Spatial Transcriptome normalization integration Seurat
updated 13 months ago by ★ 1.8k • written 13 months ago by ▴ 260
1
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2
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645
views
Visualization of Enrichment score for spatial 10x visium samples
visium transctiptome 10x enrichment scores spatial
14 months ago by Omics data mining ▴ 260
1
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2
replies
622
views
deconvolution of spatial transcriptome
deconvolution spatial transcriptome
updated 15 months ago by ★ 3.9k • written 15 months ago by ▴ 260
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1
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1.8k
views
change color and scale in SpatialFeaturePlot
clustering Seurat spatial-transcriptome
updated 15 months ago by 43k • written 15 months ago by ▴ 260
0
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0
replies
964
views
error plotting spatial data in scanpy
scanpy spatial-transcriptome
updated 15 months ago by 43k • written 15 months ago by ▴ 260
2
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0
replies
518
views
Input at BINDetect step (for TOBIAS pipeline) with multiple files
differential ATAC-Seq tobias motifs
15 months ago by Omics data mining ▴ 260
1
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6
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3.2k
views
error in pipeline installation dependent on numpy version 1.18.5
cnn numpy imaging python
15 months ago by Omics data mining ▴ 260
3
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8
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6.3k
views
bait interval list for picard collecthsmetrices
picard alignment exome
12 months ago by Omics data mining ▴ 260
1
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1
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513
views
DESeq2 with multiple conditional data
multi differential DESeq2 genes factor
updated 17 months ago by 13k • written 17 months ago by ▴ 260
8
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6
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3.2k
views
How to include spatial coordinate data into anndata within scanpy
scanpy visium transcriptome spatial 10X
updated 3 months ago by • 0 • written 19 months ago by ▴ 260
1
vote
1
reply
496
views
Batch effect of sequencing data that were sequenced in different locations
effect batch DESeq2
updated 18 months ago by 82k • written 18 months ago by ▴ 260
0
votes
0
replies
427
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
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1
reply
483
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
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563
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cluster identification and DEGs in single cell data
deg cluster seurat analysis
19 months ago by Omics data mining ▴ 260
3
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6
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1.1k
views
nested elements in bed file using awk
coordinates bedops genome awk
19 months ago by Omics data mining ▴ 260
4
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1
reply
1.1k
views
SCTransform in single cell
SCTransform seurat
updated 19 months ago by 142k • written 19 months ago by ▴ 260
1
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4
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621
views
overlap statistics among multiple bed files
bedtools
updated 10 months ago by 43k • written 19 months ago by ▴ 260
0
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2
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489
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exportFASTA not working
exportFASTA biomart getSeq
19 months ago by Omics data mining ▴ 260
0
votes
2
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522
views
Filteration of uniquely mapped reads
samtools bam
updated 10 months ago by 43k • written 20 months ago by ▴ 260
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4
replies
1.6k
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 23 months ago by ▴ 10 • written 2.1 years ago by ▴ 260
0
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0
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401
views
calculate the variance across the samples
10X spatial cell single visium
2.2 years ago by Omics data mining ▴ 260
0
votes
2
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564
views
from dexseq results to alternative splicing events identification
dexseq alternative splicing
2.2 years ago by Omics data mining ▴ 260
0
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2
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844
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
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3
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969
views
inter and intra-sample variance in 10X visium spatial transcriptome data
transcriptome cell single spatial
updated 19 months ago by 142k • written 2.2 years ago by ▴ 260
0
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5
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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
1.6k
views
gene set enrichment in clusterprofiler
clusterprofiler gene enrichment analysis set
updated 2.2 years ago by ▴ 20 • written 2.2 years ago by ▴ 260
0
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2
replies
1.4k
views
gseGO for multiple groups
clusterProfiler gseKEGG gseGO
2.2 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
833
views
impulseDE2 input
normalized count input raw impulseDE2
updated 2.3 years ago by ▴ 200 • written 2.3 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
7.4k
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
1.8k
views
UMI extraction from 10X visium spatial transcriptome data
umi_tools UMI spatial-transcriptome
updated 10 months ago by 43k • written 2.4 years ago by ▴ 260
0
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0
replies
514
views
Patient-to-patient similarities network
SNFtools multi omics
3.2 years ago by Omics data mining ▴ 260
0
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0
replies
570
views
Error running gene expression based ProTINA
ProTINA Time-Series gene-expression
updated 11 months ago by 43k • written 3.4 years ago by ▴ 260
0
votes
2
replies
973
views
Selection of SNPs after imputation
gwas imputation
updated 3.7 years ago by ▴ 140 • written 3.7 years ago by ▴ 260
0
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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
680
views
include vcf header
varscan
4.2 years ago by Omics data mining ▴ 260
1
vote
0
replies
948
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 4.3 years ago by ▴ 180 • written 5.8 years ago by ▴ 260
0
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1
reply
893
views
TCGA array expression and rnaseq expression batch correction
tcga rnaseq expression
4.6 years ago by Omics data mining ▴ 260
2
votes
2
replies
1.4k
views
Input for VariantsToBinaryPed
GATK plink
updated 4.6 years ago by 10k • written 5.9 years ago by ▴ 260
89 results • Page 1 of 2
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