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1
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890
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Can I run cellassign on samples independently if there is batch effect present?
RNA-Seq
R
cellassign
batch-effect
updated 6 months ago by
Francesco
▴ 20 • written 3.8 years ago by
gt
▴ 30
5
votes
1
reply
884
views
What should I expect to see for chromosome Y gene expression in a male mouse sample?
RNA-seq
featureCounts
STAR
updated 2.5 years ago by
Gordon Smyth
★ 7.5k • written 2.5 years ago by
gt
▴ 30
0
votes
0
replies
1.9k
views
Comment:
Comment: How to obtain all genes associated with a given GO term from PANTHER API enrichm
2.6 years ago by
gt
▴ 30
0
votes
1
reply
2.3k
views
Comment:
Comment: Statistical test on Single-cell clusters(cell types)
2.6 years ago by
gt
▴ 30
0
votes
1
reply
1.9k
views
Comment:
Comment: How to obtain all genes associated with a given GO term from PANTHER API enrichm
2.6 years ago by
gt
▴ 30
0
votes
1
reply
1.9k
views
Comment:
Comment: How to obtain all genes associated with a given GO term from PANTHER API enrichm
2.6 years ago by
gt
▴ 30
2
votes
7
replies
1.9k
views
How to obtain all genes associated with a given GO term from PANTHER API enrichment analysis
API
scRNA-seq
R
PANTHER
updated 2.0 years ago by
Viraj
• 0 • written 2.6 years ago by
gt
▴ 30
2
votes
1
reply
1.1k
views
Should I normalize the data before or after filtering to a particular cell type?
R
scRNA-seq
Seurat
updated 2.7 years ago by
Jautis
▴ 580 • written 2.7 years ago by
gt
▴ 30
0
votes
0
replies
2.0k
views
featureCounts percentage of successful assigned alignments lower than expected
RNA-seq
STAR
featureCounts
2.9 years ago by
gt
▴ 30
0
votes
0
replies
2.5k
views
Comment:
Comment: STARsolo --EmptyDrops_CR parameters
2.9 years ago by
gt
▴ 30
0
votes
0
replies
590
views
How do I access inflection points in Seurat object?
Seurat
scRNA-seq
2.9 years ago by
gt
▴ 30
0
votes
1
reply
711
views
Should I expect high duplicate read frequency in my scRNA fastq's?
scRNA-seq
fastqc
multiqc
updated 3.2 years ago by
swbarnes2
14k • written 3.2 years ago by
gt
▴ 30
0
votes
1
reply
844
views
How do I start clue GO in R using the cytoscape REST API?
API
R
cytoscape
REST
ClueGO
updated 3.2 years ago by
Scooter
▴ 280 • written 3.2 years ago by
gt
▴ 30
0
votes
0
replies
1000
views
Comment:
Comment: Low assignment rate with featureCounts
3.3 years ago by
gt
▴ 30
1
vote
2
replies
1000
views
Low assignment rate with featureCounts
featureCounts
RNA-seq
STAR
3.3 years ago by
gt
▴ 30
0
votes
0
replies
1.2k
views
Comment:
Comment: How many reads does Delly use for variant calling?
3.3 years ago by
gt
▴ 30
0
votes
0
replies
1.2k
views
Comment:
Comment: How many reads does Delly use for variant calling?
3.3 years ago by
gt
▴ 30
3
votes
4
replies
1.2k
views
How many reads does Delly use for variant calling?
DNA-seq
bwa-mem
delly
bowtie2
updated 2.5 years ago by
archanaverma433
▴ 10 • written 3.3 years ago by
gt
▴ 30
2
votes
1
reply
1.8k
views
How to filter delly variants?
calling
DNA-seq
delly
variants
updated 3.3 years ago by
trausch
★ 1.9k • written 3.3 years ago by
gt
▴ 30
0
votes
0
replies
4.4k
views
Comment:
Comment: How do I detect deletions?
3.3 years ago by
gt
▴ 30
3
votes
6
replies
4.4k
views
How do I detect deletions?
bcftools
DNA-seq
calling
variant
updated 3.3 years ago by
bernatgel
★ 3.4k • written 3.3 years ago by
gt
▴ 30
0
votes
0
replies
4.4k
views
Comment:
Comment: How do I detect deletions?
3.3 years ago by
gt
▴ 30
0
votes
1
reply
795
views
Pre-processing of BAMs before indel calling
indels
DNA-seq
bwa-mem
bowtie2
updated 3.3 years ago by
Lila M
★ 1.3k • written 3.3 years ago by
gt
▴ 30
0
votes
0
replies
653
views
How do I make bwa-mem and bowtie2 less stringent?
DNA-seq
bwa-mem
bowtie2
3.3 years ago by
gt
▴ 30
0
votes
1
reply
4.8k
views
Comment:
Comment: Filtering sam/bam by using CIGAR deletion sites
3.3 years ago by
gt
▴ 30
0
votes
0
replies
902
views
Comment:
Comment: bcftools mpileup giving more wildtypes <*> than expected
3.3 years ago by
gt
▴ 30
1
vote
2
replies
902
views
bcftools mpileup giving more wildtypes <*> than expected
bcftools
DNA-seq
mpileup
3.3 years ago by
gt
▴ 30
0
votes
0
replies
558
views
freebayes only picking up variants in a single contig
variant-calling
DNA-seq
freebayes
3.3 years ago by
gt
▴ 30
0
votes
0
replies
608
views
How to properly interpret the ALT and QUAL fields in bcf file from bcftools mpileup
bcftools
DNA-seq
mpileup
3.3 years ago by
gt
▴ 30
0
votes
0
replies
1.3k
views
Comment:
Comment: DEseq2: comparison the same when reversing factor order?
3.4 years ago by
gt
▴ 30
0
votes
1
reply
1.3k
views
Comment:
Comment: DEseq2: comparison the same when reversing factor order?
3.4 years ago by
gt
▴ 30
0
votes
4
replies
1.3k
views
DEseq2: comparison the same when reversing factor order?
DESeq2
FCROS
RNA-seq
edgeR
3.4 years ago by
gt
▴ 30
0
votes
0
replies
733
views
LOESS Normalization Explanation
proteomics
pre-processing
InfernoRDN
normalization
3.4 years ago by
gt
▴ 30
0
votes
0
replies
1.0k
views
Comment:
Comment: DESeq2: Variable Importance
3.4 years ago by
gt
▴ 30
0
votes
3
replies
1.0k
views
DESeq2: Variable Importance
DESeq2
updated 3.4 years ago by
Kevin Blighe
88k • written 3.4 years ago by
gt
▴ 30
4
votes
3
replies
2.0k
views
Deseq2 time interaction term
deseq2
rna-seq
DE
R
updated 2.4 years ago by
1769mkc
★ 1.2k • written 3.6 years ago by
gt
▴ 30
0
votes
0
replies
4.5k
views
Comment:
Comment: How to interpret multiqc report
3.6 years ago by
gt
▴ 30
0
votes
3
replies
4.5k
views
How to interpret multiqc report
QC
multiqc
rna-seq
updated 3.6 years ago by
Phil Ewels
★ 1.4k • written 3.6 years ago by
gt
▴ 30
0
votes
0
replies
2.1k
views
Comment:
Comment: featureCounts assignment low when mapping to "exon"
3.6 years ago by
gt
▴ 30
0
votes
1
reply
2.1k
views
Comment:
Comment: featureCounts assignment low when mapping to "exon"
3.6 years ago by
gt
▴ 30
2
votes
4
replies
2.1k
views
featureCounts assignment low when mapping to "exon"
RNA-seq
E.coli
featureCounts
3.6 years ago by
gt
▴ 30
0
votes
1
reply
844
views
Alignment Error in BWA: The sequence "lcl|" was not found
bwa
DNA-Seq
alignment
3.7 years ago by
gt
▴ 30
0
votes
0
replies
1.0k
views
Comment:
C: How do I know bcftools mpileup command completed?
3.7 years ago by
gt
▴ 30
0
votes
1
reply
1.0k
views
Comment:
A: How do I know bcftools mpileup command completed?
3.7 years ago by
gt
▴ 30
0
votes
4
replies
1.0k
views
How do I know bcftools mpileup command completed?
bcftools
mpileup
DNA-seq
3.7 years ago by
gt
▴ 30
2
votes
1
reply
837
views
bcftools command not working
bcftools
dna-seq
SNP
updated 3.7 years ago by
GenoMax
147k • written 3.7 years ago by
gt
▴ 30
0
votes
0
replies
662
views
STAR Alignment for E. Coli: Segmentation Error
RNA-Seq
STAR
alignment
software error
3.8 years ago by
gt
▴ 30
0
votes
0
replies
1.7k
views
Comment:
C: Should I integrate datasets between conditions if I am doing differential expres
3.9 years ago by
gt
▴ 30
0
votes
0
replies
1.7k
views
Comment:
C: Should I integrate datasets between conditions if I am doing differential expres
3.9 years ago by
gt
▴ 30
0
votes
1
reply
1.7k
views
Comment:
C: Should I integrate datasets between conditions if I am doing differential expres
3.9 years ago by
gt
▴ 30
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