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25 results • Page
1 of 1
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Rank
Views
Votes
Replies
0
votes
0
replies
30
views
Quetion regarding WGCNA
WGCNA
Network
construction
2 hours ago by
deepak180001
• 0
0
votes
0
replies
31
views
Design matrix Differential expression analysis
expression
designmatrix
analysis
Differential
RNA-sequence
3 hours ago by
SHN
▴ 40
0
votes
0
replies
41
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
4 hours ago by
Ximena
• 0
0
votes
0
replies
38
views
filtering before dada2
metagenomic
bbduk
qiime2
dada2
bioinformatics
4 hours ago by
Valentina
• 0
0
votes
6
replies
244
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 4 hours ago by
swbarnes2
14k • written 11 hours ago by
Erina
• 0
0
votes
1
reply
70
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 6 hours ago by
GenoMax
142k • written 7 hours ago by
Lada
▴ 30
0
votes
0
replies
55
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
8 hours ago by
Emilie
• 0
0
votes
0
replies
51
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
9 hours ago by
Javier
• 0
0
votes
0
replies
44
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
9 hours ago by
yahn
• 0
0
votes
0
replies
52
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
9 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
52
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 9 hours ago by
Ram
43k • written 9 hours ago by
M.
▴ 30
0
votes
2
replies
106
views
Raw counts using stringtie
stringtie
RNA-seq
updated 9 hours ago by
GenoMax
142k • written 10 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
49
views
Modify plot R mtDNA indel
plot
mtDNA
R
11 hours ago by
marco.barr
▴ 90
0
votes
0
replies
54
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
11 hours ago by
NorbertK
• 0
0
votes
1
reply
94
views
Downloading older version of a tool
Alignment
tools
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
Ruqaiya
• 0
0
votes
0
replies
64
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
13 hours ago by
rustykb
▴ 20
3
votes
5
replies
179
views
Generating mpileup file using samtools
mpileup
samtools
updated 12 hours ago by
Joe
21k • written 15 hours ago by
Ruqaiya
• 0
1
vote
3
replies
174
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 9 hours ago by
dthorbur
★ 1.9k • written 18 hours ago by
Vijith
▴ 30
0
votes
0
replies
81
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
19 hours ago by
Jeyong
• 0
0
votes
0
replies
78
views
Empty table plot using plotGseaTable()
FGSEA
4 hours ago by
Chris
▴ 260
0
votes
1
reply
164
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 22 hours ago by
Chris Dean
▴ 390 • written 1 day ago by
sovrappensiero
▴ 90
1
vote
3
replies
211
views
Odd alignment question/finding
Alignment
updated 15 hours ago by
barslmn
★ 2.1k • written 1 day ago by
poordumbsillyidiot
• 0
1
vote
6
replies
321
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 9 hours ago by
GenoMax
142k • written 18 days ago by
eebloom
▴ 80
0
votes
1
reply
542
views
HOMER on AWS
HOMER
updated 21 hours ago by
clairechung112
• 0 • written 2.2 years ago by
Bogdan
★ 1.4k
2
votes
2
replies
1.7k
views
Parametric or non-parametric tests for qPCR significance testing between treatments?
qPCR
statistical test
parametric
non-parametric
updated 6 hours ago by
e.r.zakiev
▴ 210 • written 3.8 years ago by
n.anuragsharma
▴ 40
25 results • Page
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Recent Votes
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
Comment: No INFO/info value in headers
how to combine multiple RNAseq count files into a single dataframe in R and unix
Comment: Greatly speed up conda by using mamba
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▴ 170
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GenoMax
142k
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Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Mbofire
• 0
I need assistance don't know what to do next after signing up
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
Comment: Parametric or non-parametric tests for qPCR significance testing between treatme
by
e.r.zakiev
▴ 210
obviously if the values are really sampled from a (quasi) normally-distributed values, then n doesn't matter, he could use t-test even with…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
Understood Thank you!
Comment: Converting CRAM to FastQ
by
GenoMax
142k
You can use any reference that you like at this point. Since you are planning to use GATK, you can get their version from the resource bund…
Comment: Converting CRAM to FastQ
by
Maverick
▴ 10
![enter image description here][1]I was able to get my fastq files. I can see that my reference files are cached in a hts-ref directory but…
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Okay, that shows us the problem, but not what we need to solve it. But, for instance, are you sure that period after the sample name shou…
Comment: Easy way to find out which allele is minor allele from bed file?
by
bk11
★ 2.4k
In the case of MAF = 0.5, I think A1 is still the minor allele. You can check the discussion in this [link][1]. [1]: https://groups.goo…
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