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Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq R cellassign batch-effect
updated 9 months ago by ▴ 20 • written 4.1 years ago by ▴ 30
5
votes
1
reply
974
views
What should I expect to see for chromosome Y gene expression in a male mouse sample?
RNA-seq featureCounts STAR
updated 2.8 years ago by ★ 7.8k • written 2.8 years ago by ▴ 30
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0
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2.2k
views
Comment: Comment: How to obtain all genes associated with a given GO term from PANTHER API enrichm
2.9 years ago by gt ▴ 30
0
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1
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2.4k
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Comment: Comment: Statistical test on Single-cell clusters(cell types)
2.9 years ago by gt ▴ 30
0
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1
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2.2k
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Comment: Comment: How to obtain all genes associated with a given GO term from PANTHER API enrichm
2.9 years ago by gt ▴ 30
0
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1
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2.2k
views
Comment: Comment: How to obtain all genes associated with a given GO term from PANTHER API enrichm
2.9 years ago by gt ▴ 30
2
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7
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2.2k
views
How to obtain all genes associated with a given GO term from PANTHER API enrichment analysis
API scRNA-seq R PANTHER
updated 2.3 years ago by • 0 • written 2.9 years ago by ▴ 30
2
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1
reply
1.3k
views
Should I normalize the data before or after filtering to a particular cell type?
R scRNA-seq Seurat
updated 2.9 years ago by ▴ 580 • written 2.9 years ago by ▴ 30
0
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0
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2.0k
views
featureCounts percentage of successful assigned alignments lower than expected
RNA-seq STAR featureCounts
3.2 years ago by gt ▴ 30
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0
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2.7k
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Comment: Comment: STARsolo --EmptyDrops_CR parameters
3.2 years ago by gt ▴ 30
0
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0
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631
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How do I access inflection points in Seurat object?
Seurat scRNA-seq
3.2 years ago by gt ▴ 30
0
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1
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766
views
Should I expect high duplicate read frequency in my scRNA fastq's?
scRNA-seq fastqc multiqc
updated 3.4 years ago by 14k • written 3.4 years ago by ▴ 30
0
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1
reply
902
views
How do I start clue GO in R using the cytoscape REST API?
API R cytoscape REST ClueGO
updated 3.5 years ago by ▴ 280 • written 3.5 years ago by ▴ 30
0
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0
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1.1k
views
Comment: Comment: Low assignment rate with featureCounts
3.5 years ago by gt ▴ 30
1
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2
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1.1k
views
Low assignment rate with featureCounts
featureCounts RNA-seq STAR
3.5 years ago by gt ▴ 30
0
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0
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1.3k
views
Comment: Comment: How many reads does Delly use for variant calling?
3.6 years ago by gt ▴ 30
0
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0
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1.3k
views
Comment: Comment: How many reads does Delly use for variant calling?
3.6 years ago by gt ▴ 30
3
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4
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1.3k
views
How many reads does Delly use for variant calling?
DNA-seq bwa-mem delly bowtie2
updated 2.8 years ago by ▴ 10 • written 3.6 years ago by ▴ 30
2
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1
reply
2.0k
views
How to filter delly variants?
calling DNA-seq delly variants
updated 3.6 years ago by ★ 1.9k • written 3.6 years ago by ▴ 30
0
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0
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5.0k
views
Comment: Comment: How do I detect deletions?
3.6 years ago by gt ▴ 30
3
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6
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5.0k
views
How do I detect deletions?
bcftools DNA-seq calling variant
updated 3.6 years ago by ★ 3.4k • written 3.6 years ago by ▴ 30
0
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0
replies
5.0k
views
Comment: Comment: How do I detect deletions?
3.6 years ago by gt ▴ 30
0
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1
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874
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Pre-processing of BAMs before indel calling
indels DNA-seq bwa-mem bowtie2
updated 3.6 years ago by ★ 1.3k • written 3.6 years ago by ▴ 30
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0
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699
views
How do I make bwa-mem and bowtie2 less stringent?
DNA-seq bwa-mem bowtie2
3.6 years ago by gt ▴ 30
0
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1
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5.0k
views
Comment: Comment: Filtering sam/bam by using CIGAR deletion sites
3.6 years ago by gt ▴ 30
0
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0
replies
968
views
Comment: Comment: bcftools mpileup giving more wildtypes <*> than expected
3.6 years ago by gt ▴ 30
1
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2
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968
views
bcftools mpileup giving more wildtypes <*> than expected
bcftools DNA-seq mpileup
3.6 years ago by gt ▴ 30
0
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0
replies
596
views
freebayes only picking up variants in a single contig
variant-calling DNA-seq freebayes
3.6 years ago by gt ▴ 30
0
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0
replies
661
views
How to properly interpret the ALT and QUAL fields in bcf file from bcftools mpileup
bcftools DNA-seq mpileup
3.6 years ago by gt ▴ 30
0
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0
replies
1.4k
views
Comment: Comment: DEseq2: comparison the same when reversing factor order?
3.6 years ago by gt ▴ 30
0
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1
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1.4k
views
Comment: Comment: DEseq2: comparison the same when reversing factor order?
3.6 years ago by gt ▴ 30
0
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4
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1.4k
views
DEseq2: comparison the same when reversing factor order?
DESeq2 FCROS RNA-seq edgeR
3.6 years ago by gt ▴ 30
0
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0
replies
775
views
LOESS Normalization Explanation
proteomics pre-processing InfernoRDN normalization
3.7 years ago by gt ▴ 30
0
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0
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1.1k
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Comment: Comment: DESeq2: Variable Importance
3.7 years ago by gt ▴ 30
0
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3
replies
1.1k
views
DESeq2: Variable Importance
DESeq2
updated 3.7 years ago by 89k • written 3.7 years ago by ▴ 30
4
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3
replies
2.2k
views
Deseq2 time interaction term
deseq2 rna-seq DE R
updated 2.7 years ago by ★ 1.2k • written 3.9 years ago by ▴ 30
0
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0
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5.0k
views
Comment: Comment: How to interpret multiqc report
3.9 years ago by gt ▴ 30
0
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3
replies
5.0k
views
How to interpret multiqc report
QC multiqc rna-seq
updated 3.8 years ago by ★ 1.4k • written 3.9 years ago by ▴ 30
0
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0
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2.2k
views
Comment: Comment: featureCounts assignment low when mapping to "exon"
3.9 years ago by gt ▴ 30
0
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1
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2.2k
views
Comment: Comment: featureCounts assignment low when mapping to "exon"
3.9 years ago by gt ▴ 30
2
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4
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2.2k
views
featureCounts assignment low when mapping to "exon"
RNA-seq E.coli featureCounts
3.9 years ago by gt ▴ 30
0
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1
reply
879
views
Alignment Error in BWA: The sequence "lcl|" was not found
bwa DNA-Seq alignment
4.0 years ago by gt ▴ 30
0
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0
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1.1k
views
Comment: C: How do I know bcftools mpileup command completed?
4.0 years ago by gt ▴ 30
0
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4
replies
1.1k
views
How do I know bcftools mpileup command completed?
bcftools mpileup DNA-seq
4.0 years ago by gt ▴ 30
0
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1
reply
1.1k
views
Comment: A: How do I know bcftools mpileup command completed?
4.0 years ago by gt ▴ 30
2
votes
1
reply
886
views
bcftools command not working
bcftools dna-seq SNP
updated 4.0 years ago by 149k • written 4.0 years ago by ▴ 30
0
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0
replies
698
views
STAR Alignment for E. Coli: Segmentation Error
RNA-Seq STAR alignment software error
4.0 years ago by gt ▴ 30
0
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0
replies
1.8k
views
Comment: C: Should I integrate datasets between conditions if I am doing differential expres
4.1 years ago by gt ▴ 30
0
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0
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1.8k
views
Comment: C: Should I integrate datasets between conditions if I am doing differential expres
4.1 years ago by gt ▴ 30
0
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1
reply
1.8k
views
Comment: C: Should I integrate datasets between conditions if I am doing differential expres
4.1 years ago by gt ▴ 30
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