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5
votes
2
replies
5.6k
views
How should I interpret this Mummer output files?
mapping mummer show-coords
updated 22 months ago by ▴ 20 • written 9.9 years ago by ▴ 690
1
vote
2
replies
3.0k
views
ERRBS Methylation data analysis
next-gen Bisulfite methylation homer ERRBS
updated 20 months ago by 43k • written 8.5 years ago by ▴ 690
2
votes
3
replies
3.0k
views
Can we crosscheck log2 fold change in gene expression data?
RNA-Seq
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 690
1
vote
3
replies
2.8k
views
Best software to identify differentially methylated regions in Chipseq data?
ChIP-Seq differentially methylated genes
updated 23 months ago by 43k • written 9.6 years ago by ▴ 690
5
votes
5
replies
4.1k
views
[DESeq2 multiple treatments vs. 1-by-1] Inconsistant p-adj
RNA-Seq deseq2
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 690
2
votes
4
replies
3.8k
views
Cummerbund Returns 0 Sample
cuffdiff cummerbund
updated 6.6 years ago by ▴ 10 • written 10.2 years ago by ▴ 690
0
votes
1
reply
4.1k
views
WGCNA defining parameters for soft threshold in R?
WGCNA R
updated 15 months ago by 43k • written 9.0 years ago by ▴ 690
4
votes
6
replies
11k
views
Cnvnator Output File
updated 7.1 years ago by ▴ 10 • written 12.0 years ago by ▴ 690
6
votes
6
replies
5.7k
views
[Samtools] How to extract reads matching a given sequence
alignment samtools sequence sequencing
updated 2.6 years ago by 43k • written 10.0 years ago by ▴ 690
8
votes
7
replies
11k
views
DESeq2 very high p-values and padj
DESeq2 p-values RNA-Seq
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 690
2
votes
11
replies
3.3k
views
BWA batch script does not execute
bwa
updated 8.0 years ago by ★ 3.8k • written 8.0 years ago by ▴ 690
7
votes
14
replies
7.1k
views
How to align 100 samples with BWA?
next-gen exome alignment bwa
updated 8.1 years ago by 12k • written 8.1 years ago by ▴ 690
2
votes
10
replies
7.5k
views
Samtools Error Message, Please Help !
samtools bam sam
updated 8.1 years ago by 20 • written 11.9 years ago by ▴ 690
19
votes
5
replies
9.1k
views
Is There A Tool (Samtools, Picard ..) To Filter Certain Flags In Bam File ?
samtools bam
updated 8.2 years ago by 20 • written 11.9 years ago by ▴ 690
4
votes
5
replies
4.4k
views
Need help with heatmap.2
heatmap RNA-Seq
updated 2.3 years ago by 43k • written 9.8 years ago by ▴ 690
0
votes
0
replies
1.8k
views
Which software/algorithm do you use to analyze methylation data
bisulfilte sequencing methylation
updated 20 months ago by 43k • written 8.5 years ago by ▴ 690
0
votes
2
replies
3.6k
views
Spotfire: Issue when creating heat maps
microarray spotfire heatmap
updated 22 months ago by 43k • written 9.1 years ago by ▴ 690
1
vote
3
replies
5.1k
views
WGCNA how to pick the soft threshold with R
WGCNA R
updated 9.0 years ago by 5.1k • written 9.0 years ago by ▴ 690
2
votes
14
replies
9.6k
views
Batch Effect normalization with Combat generates error
microarray normalization combat
updated 15 months ago by 43k • written 9.0 years ago by ▴ 690
2
votes
1
reply
15k
views
How to use Combat in R??
R software-error Combat
updated 15 months ago by 43k • written 9.0 years ago by ▴ 690
0
votes
0
replies
3.2k
views
How to build similarity matrix in WGCNA?
r software-error wgcna matrix
updated 15 months ago by 43k • written 9.0 years ago by ▴ 690
6
votes
2
replies
4.6k
views
What pipeline should I use with WGCNA?
WGCNA
updated 3 months ago by ▴ 20 • written 9.0 years ago by ▴ 690
1
vote
1
reply
3.3k
views
Soft threshold in WGCNA
wgcna
updated 15 months ago by 43k • written 9.0 years ago by ▴ 690
2
votes
3
replies
3.0k
views
DESeq2 - Warning message
deseq2 RNA-Seq software-error R
updated 15 months ago by 43k • written 9.0 years ago by ▴ 690
1
vote
1
reply
3.7k
views
How to use ToppGene ??
gene-expression RNAseq toppgene
updated 15 months ago by 43k • written 9.1 years ago by ▴ 690
3
votes
4
replies
7.4k
views
Having trouble creating a heatmap in SPOTFIRE (microarray data)
microarray spotfire heatmap
updated 22 months ago by 43k • written 9.1 years ago by ▴ 690
2
votes
2
replies
2.9k
views
Analyze miRNA microarrays
microarray miRNA-analysis
updated 23 months ago by 43k • written 9.1 years ago by ▴ 690
6
votes
5
replies
6.8k
views
BCFtools outputs error : [bcf_sync] incorrect number of fields (6 != 5)
bcftools samtools mpileup BAM
updated 2.5 years ago by 43k • written 9.9 years ago by ▴ 690
0
votes
0
replies
3.4k
views
How to cluster only genes with Cluster 3.0 ?
treeview cluster
updated 2.3 years ago by 43k • written 9.6 years ago by ▴ 690
8
votes
6
replies
16k
views
log2 fold change : how to cut out by two fold?
log2 RNA-Seq
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 690
4
votes
4
replies
7.4k
views
How to create a SIF file to use in Cytoscape?
cytoscape interaction gene
updated 9.7 years ago by 161k • written 9.7 years ago by ▴ 690
1
vote
6
replies
8.6k
views
How to Generate GO annotation from list of genes
gene-ontology blast2go
updated 2.4 years ago by 43k • written 9.7 years ago by ▴ 690
3
votes
1
reply
7.5k
views
deseq2 how to define data.frame with multiple treatments and multiple replicates?
RNA-Seq heatmap deseq2
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 690
6
votes
1
reply
7.5k
views
Is there a good manual/tutorial for TreeView?
heatmap RNAseq treeview
updated 2.4 years ago by 43k • written 9.8 years ago by ▴ 690
9
votes
7
replies
14k
views
DESeq2 doesn't compare the right ctrl vs treatment?
DESeq2 RNA-Seq
updated 2.5 years ago by 43k • written 9.8 years ago by ▴ 690
7
votes
5
replies
29k
views
Error: could not find function "heatmap.2"
deseq2 RNA-Seq heatmap
updated 2.5 years ago by 43k • written 9.8 years ago by ▴ 690
0
votes
4
replies
5.2k
views
How can I use SNPeff with this genome?
snpeff SNP
updated 2.5 years ago by 43k • written 9.8 years ago by ▴ 690
0
votes
0
replies
1.5k
views
What's a good Variant effect predictor for draft genomes?
genome variant SNP non-synonymous predictor
updated 2.5 years ago by 43k • written 9.9 years ago by ▴ 690
5
votes
1
reply
8.4k
views
Calling heterozygous and homozygous SNPs with SAMtools or VCF ?
vcf heterozygous bam samtools SNP
updated 2.3 years ago by 43k • written 9.9 years ago by ▴ 690
0
votes
2
replies
2.4k
views
[Samtools] How many hours does it take to call SNPs and indels?
time samtools bam
updated 2.5 years ago by 43k • written 9.9 years ago by ▴ 690
1
vote
3
replies
14k
views
[samtools depth] Calculate percent of the genome covered
samtools bam genome coverage
updated 2.3 years ago by 43k • written 9.9 years ago by ▴ 690
4
votes
3
replies
4.0k
views
[samtools reheader] Can't change chromosome name
samtools bam reheader
updated 2.6 years ago by 43k • written 9.9 years ago by ▴ 690
5
votes
3
replies
2.5k
views
How To Build Gene Network Biology ?
gene network biology
updated 10.2 years ago by 20 • written 12.0 years ago by ▴ 690
1
vote
1
reply
3.5k
views
Cummerbund Help
cummerbund r
updated 10.2 years ago by ▴ 890 • written 10.2 years ago by ▴ 690
3
votes
2
replies
16k
views
Cuffdiff Output Interpretation
cuffdiff differential-expression
10.2 years ago by madkitty ▴ 690
0
votes
0
replies
3.1k
views
Can I Call Cnvs On All Chromosome With Cnvnator ?
cnv
updated 10.6 years ago by 20 • written 12.0 years ago by ▴ 690
22
votes
10
replies
16k
views
6 follow
How To Get The Read Depth?
genome sequencing read depth-of-coverage
updated 11.7 years ago by 22k • written 11.7 years ago by ▴ 690
0
votes
4
replies
2.1k
views
Breakdancer -Q Flag Doesn'T Work
breakdancer cnv
updated 11.8 years ago by 11k • written 11.8 years ago by ▴ 690
0
votes
2
replies
2.6k
views
Breakdancer Options, Unconsistency Please Help!
breakdancer cnv
updated 11.8 years ago by 22k • written 11.8 years ago by ▴ 690
1
vote
1
reply
3.0k
views
Breakdancer Options For Minimum Quality Mapping
breakdancer cnv
updated 11.8 years ago by 22k • written 11.8 years ago by ▴ 690
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