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0
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0
replies
234
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What does ANOVA test over CoxPH model mean?
SurvivalAnalysis
CoxPH
ANOVA
Survival
3 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
0
replies
780
views
Comment:
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
5 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
780
views
Comment:
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
5 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
780
views
Comment:
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
5 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
5.9k
views
Comment:
Comment: How to create interval list from reference fasta or dict file?
5 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
6
replies
780
views
GetPileupSummaries intervals-list with Targeted Sequencing?
GetPileUpSummaries
GATK
Variant-Calling
updated 5 months ago by
Ram
43k • written 5 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
288
views
Apply BSQR for Targeted Sequencing
GenomicPipelines
GATK
variant-calling
5 months ago by
Manuel Sokolov Ravasqueira
▴ 100
4
votes
2
replies
691
views
Visualization package for Maf Files using Python
Python
maftools
Visualization
MAF
updated 7 months ago by
Mark
★ 1.5k • written 7 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
335
views
Convert from limma voom normalized matrix each gene to high/low
limma-voom
RNA-SEQ
updated 7 months ago by
Ram
43k • written 7 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
1
reply
633
views
Consensus Cluster takes normalized gene counts or raw gene counts?
R
Gene-Expression
ConsensusCluster
DGE
updated 8 months ago by
bk11
★ 2.5k • written 8 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.3k
views
Comment:
Comment: Enricher - Hyper Geometric Test Details
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.3k
views
Comment:
Comment: Enricher - Hyper Geometric Test Details
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.3k
views
Comment:
Comment: Enricher - Hyper Geometric Test Details
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.3k
views
Comment:
Comment: Enricher - Hyper Geometric Test Details
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
6
votes
9
replies
1.3k
views
Enricher - Hyper Geometric Test Details
Enricher
ClusterProfiler
DGE
ORA
updated 9 months ago by
ATpoint
82k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
0
replies
579
views
Answer:
Answer: Over Representation Analysis over one specific pathway
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
579
views
Comment:
Comment: Over Representation Analysis over one specific pathway
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
3
votes
3
replies
579
views
Over Representation Analysis over one specific pathway
GSEA
DGE
ORA
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
1
reply
647
views
Enricher with Gene Symbols
DGE
ClusterProfiler
Enrich
ORA
updated 9 months ago by
bk11
★ 2.5k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
0
replies
291
views
How to define TMB-High/TMB-Low and Gene Expression High/Low?
Voom
Limma
TMB
RNASeq
GeneExpression
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
601
views
Comment:
Comment: Gene set enrichment analysis / Kegg analysis
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
746
views
Comment:
Comment: What are the reasons to find so few Differentially expressed genes (DEGs)?
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
1
reply
771
views
Comment:
Comment: LogFc vs t_statistic to estimate over/under expressed genes?
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
8
votes
4
replies
771
views
LogFc vs t_statistic to estimate over/under expressed genes?
T-Test
Limma
DGE
Voom
updated 9 months ago by
ATpoint
82k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
2
votes
1
reply
594
views
Maf File Bar Code
GATK
Maf
vcf
updated 9 months ago by
Zhenyu Zhang
★ 1.2k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
11
votes
3
replies
555
views
Send BAM files from server to cluster
BAM
updated 9 months ago by
ATpoint
82k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
4
votes
5
replies
709
views
Keplen Meyer Curve Dropping to zero
R
SurvivalAnalysis
SurvFit
Surv
updated 9 months ago by
Shred
★ 1.4k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
709
views
Comment:
Comment: Keplen Meyer Curve Dropping to zero
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.1k
views
Comment:
Comment: GATK GetPileupSummaries Java heap space
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
1
reply
1.9k
views
Comment:
Comment: Typical Volcano Plot for DGE
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
8
replies
1.3k
views
6 follow
Convert files made for b37 into hg19 human reference?
GATK
Variant-Calling
Mutect2
updated 9 months ago by
Ming Tommy Tang
★ 3.9k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
0
replies
1.9k
views
Answer:
Answer: Typical Volcano Plot for DGE
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.1k
views
Comment:
Comment: GATK GetPileupSummaries Java heap space
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
7
votes
5
replies
1.1k
views
GATK GetPileupSummaries Java heap space
GATK
Variant-Calling
GetPileupSummaries
updated 5 months ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
542
views
GATK GetPileUpSummariesUsage
GATK
Variant-Calling
Mutect2
GetPileupSummaries
updated 9 months ago by
Ram
43k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
5.9k
views
Comment:
Comment: GATK BaseRecalibrator known-sites vcf file
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
5.9k
views
Comment:
Comment: GATK BaseRecalibrator known-sites vcf file
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
12k
views
Comment:
Comment: problems in hg19 and b37 compatibility
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
1.3k
views
Comment:
Comment: Convert files made for b37 into hg19 human reference?
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
1.3k
views
Comment:
Comment: Convert files made for b37 into hg19 human reference?
9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
906
views
Does the gene universe for enrichGo need to be a list of gene names?
enrichGo
RNA-Seq
OverRepresentation
ORA
clusterProfiler
updated 9 months ago by
Basti
★ 2.0k • written 9 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
932
views
Comment:
Comment: GATK Mutect2 Input files reference and features have incompatible contigs: No ov
10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
932
views
Comment:
Comment: GATK Mutect2 Input files reference and features have incompatible contigs: No ov
10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
2
replies
932
views
Comment:
Comment: GATK Mutect2 Input files reference and features have incompatible contigs: No ov
10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
1
vote
7
replies
932
views
GATK Mutect2 Input files reference and features have incompatible contigs: No overlapping contigs found.
hg19
Mutect2
GATK
Variant-Calling
updated 7 weeks ago by
Ram
43k • written 10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
525
views
Comment:
Comment: Should sorted bam files when processed have ordered chromossomes?
10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
525
views
Comment:
Comment: Should sorted bam files when processed have ordered chromossomes?
10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
5
votes
5
replies
525
views
Should sorted bam files when processed have ordered chromossomes?
BAM
GATK
MarkDuplicates
updated 10 months ago by
Ram
43k • written 10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
679
views
Comment:
Comment: Filtering unmapped reads from BAM files
10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
6
votes
3
replies
580
views
Optimal Over Representation Analysis DE genes foldFC threshold?
ClusterProfiler
ORA
EnrichGo
DGE
updated 10 months ago by
LauferVA
4.2k • written 10 months ago by
Manuel Sokolov Ravasqueira
▴ 100
57 results • Page
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