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27 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
1
vote
2
replies
39
views
MA plot of shrunken fold change
MA
plot
Deseq2
1 hour ago by
Sudip
• 0
1
vote
1
reply
29
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
count
file
error
in
feature
updated 34 minutes ago by
Michael
54k • written 1 hour ago by
Ravita
• 0
0
votes
0
replies
18
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
2 hours ago by
Adyasha
• 0
0
votes
0
replies
35
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
5 hours ago by
fanglujing
▴ 60
0
votes
0
replies
51
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
7 hours ago by
Jacob
• 0
0
votes
1
reply
92
views
Differential Accessibility
DiffBind
updated 11 hours ago by
Ram
43k • written 12 hours ago by
Shloka
• 0
0
votes
2
replies
135
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
6 hours ago by
kim
• 0
3
votes
7
replies
216
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
15 hours ago by
salias
• 0
0
votes
0
replies
58
views
Using limma in methylation EM-seq?
EM-seq
methylation
17 hours ago by
Lluís R.
★ 1.2k
0
votes
0
replies
67
views
Synteny analysis
bacterial
synteny
genome
updated 17 hours ago by
GenoMax
141k • written 17 hours ago by
Namil
• 0
0
votes
4
replies
117
views
Genbank File Format
gbkformat
37 minutes ago by
alenew.am
• 0
0
votes
0
replies
132
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
18 hours ago by
SSSJec
• 0
0
votes
3
replies
159
views
Software to separate reads from different individuals
software
development
nanopore
updated 13 hours ago by
GenoMax
141k • written 18 hours ago by
njornet
▴ 20
0
votes
0
replies
60
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
18 hours ago by
David
• 0
0
votes
2
replies
125
views
How to update R on ubuntu
installation
update
R
apt-get
18 hours ago by
Bosberg
▴ 50
0
votes
0
replies
77
views
LEfSe
LEfSe
21 hours ago by
benkosta
• 0
0
votes
0
replies
65
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
19 hours ago by
Sara
▴ 30
0
votes
2
replies
117
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
22 hours ago by
Lluís R.
★ 1.2k
0
votes
2
replies
163
views
What should I consider as FASTA for dataset?
PDB
FASTA
12 hours ago by
Nafi
• 0
0
votes
0
replies
80
views
vg call vs vg surject
vg
variation
graphs
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
aliraza3119
• 0
0
votes
1
reply
108
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 20 hours ago by
GenoMax
141k • written 1 day ago by
Winter
• 0
0
votes
0
replies
106
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 17 hours ago by
dariober
14k • written 2 days ago by
rene.j.erhardt
▴ 20
1
vote
7
replies
363
views
Downsampling fastq file
downsample
fastq
updated 17 hours ago by
Ram
43k • written 7 days ago by
marco.barr
▴ 80
0
votes
3
replies
311
views
CWl and toil singularity image e.g busybox? Thank you
toil
singularity
updated 17 hours ago by
Ram
43k • written 4 months ago by
Fadi
• 0
2
votes
5
replies
917
views
Retrieval of Active site information programmatically
Catalytic
Python
Active
PDB
site
Site
updated 15 hours ago by
Wayne
★ 2.0k • written 2.0 years ago by
arinjoy
• 0
4
votes
9
replies
2.1k
views
Legend and hap files for imputation with 38 build
reference
38build
impute
imputation
15 hours ago by
anna
▴ 20
1
vote
6
replies
2.8k
views
Segmentation fault using gemma
gemma
gwas
updated 20 hours ago by
dimpleadiwal050896
• 0 • written 4.9 years ago by
ggman
▴ 90
27 results • Page
1 of 1
Recent Votes
Answer: blasting genome contigs against local SILVA 16S RNA database
blasting genome contigs against local SILVA 16S RNA database
Comment: Integrate transcriptomic data and proteomics data.
Comment: MA plot of shrunken fold change
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
Answer: How to find rna strand direction before alignment?
How to work out Z score for heatmaps for RNA seq dataset
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Recent Awards •
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Popular Question
to
kamhamea
• 0
Teacher
to
ATpoint
82k
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fanglujing
▴ 60
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geneontologyhelp
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Gordon Smyth
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Recent Replies
Answer: Deseq2
by
Jack Tierney
▴ 360
[This vignette][1] is a great place to start. [1]: https://bioconductor.org/packages/devel/bioc/vignettes/DESeq2/inst/doc/DESeq2.ht…
Comment: Genbank File Format
by
alenew.am
• 0
Thanks, yes i have tried first here looking for a easier solution (for me), i didnt' know if this format was already available somewhere. t…
Comment: Genbank File Format
by
alenew.am
• 0
Yes, it would be fine with an external solution, thanks for the reply
Answer: Polishing genome assembly
by
Michael
54k
If you have Hifi reads your error rate should already be quite good, therefore polishing with potentially longer and slightly more error-pr…
Comment: Integrate transcriptomic data and proteomics data.
by
Lluís R.
★ 1.2k
You don't need to subset for common features, there are tools that work for that like RGCCA, mixOmics. See for instance a classification [h…
Answer: Integrate transcriptomic data and proteomics data.
by
KABILAN
▴ 50
You can use R package named 'mixOmics' to integrate the datasets. Kindly go through the manual of this package.
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Michael
54k
You will have to describe your problem in much more detail, we are unable to understand what the problem even is. > Please, anyone, sugge…
Comment: MA plot of shrunken fold change
by
Sudip
• 0
Thank you.
Comment: MA plot of shrunken fold change
by
ATpoint
82k
You will need to relevel to make all comparisons available as coefficients, see https://www.biostars.org/p/448959/, or just use ashr shrink…
Comment: Integrate transcriptomic data and proteomics data.
by
ATpoint
82k
I have yet to see the fancy integration tool that can really do anything other than subsetting both datasets to the common genes/proteins/p…
Comment: Integrate transcriptomic data and proteomics data.
by
Ram
43k
Please define "combine" and "integrate" as best as you can. How do you picture the final product of this task?
Comment: NGS forensics: how to know if data is fabricated
by
Philipp Bayer
8.4k
just k-mer counts (HashingVectorizer + Naive Bayes Classifier). I stayed away from looking at quality scores so far, simulators are usually…
Comment: Landmark gene selection in L1000.
by
kim
• 0
thank you for reply, but i want some information for what microarray data are selected for L1000. thank you!
Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
weidonglu
• 0
The reason for your problem was most likely due to you relative complex data and too little system memory. For 20000-30000 transcriptome se…
Comment: Perfom a Gene Ontology Analysis from GO terms txt file
by
sansan_96
▴ 80
Your table should look like this (GO terms): ``` geneid GOid Zm00001eb000010 GO:0003690;GO:0003727;GO:0019843;GO:0005739 Zm00001eb000020 G…
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