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101,924 results • Page
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How can I find a DNA sequence that codes for a protein from a large FASTQ file?
conversion
protein
FASTQ
extinct
macOS
mammoth
updated 43 minutes ago by
cmdcolin
★ 2.1k • written 4 hours ago by
01167507
▴ 10
2
votes
8
replies
92
views
How to regress out age and sex using limma removeBatchEffect
removeBatchEffect
expression
data
Limma
40 minutes ago by
aropri
▴ 80
0
votes
0
replies
28
views
What LOH means in CANVAS
CANVAS
2 hours ago by
ManuelDB
▴ 30
0
votes
0
replies
21
views
Understanding the output generated using rehh package
sfs
Rehh
2 hours ago by
taniamahmood38
▴ 20
1
vote
1
reply
62
views
How to access the ACLAME server?
.
updated 2 hours ago by
GenoMax
115k • written 4 hours ago by
cloredana20
• 0
0
votes
0
replies
40
views
How to do RNA-Seq metadata analysis?
RNA-Seq
metadata
4 hours ago by
Francois Piumi
▴ 30
4
votes
11
replies
213
views
Automatic rename of filenames with bash script
rename
bash
script
updated 7 hours ago by
cpad0112
20k • written 9 hours ago by
Morta
• 0
0
votes
7
replies
1.6k
views
6 follow
Picrust2: High level of description
picrust
picrust2
updated 8 hours ago by
Ghildan
• 0 • written 19 months ago by
Claire
• 0
670
votes
160
replies
84k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 5 weeks ago by
Biostar
730 • written 5.5 years ago by
Istvan Albert
93k
1
vote
1
reply
67
views
Compare the samples in a VCF
variation
updated 8 hours ago by
Pierre Lindenbaum
145k • written 9 hours ago by
marzieh
• 0
1
vote
3
replies
97
views
How to add the ancestral allele (AA) information in a vcf file?
AA_tag
vcf
updated 5 hours ago by
Pierre Lindenbaum
145k • written 9 hours ago by
taniamahmood38
▴ 20
1
vote
6
replies
826
views
How to do Microarray Metadata analysis using R
metadata
R
microarray
packages
rstudio
updated 9 hours ago by
mrashad
▴ 60 • written 12 months ago by
xxxxxxxx
▴ 20
7
votes
1
reply
181
views
News:
NGSymposium - Conference in Computational Biology, 23-24.09
ML
statistics
conference
ngschool
9 hours ago by
kzkedzierska
▴ 290
0
votes
2
replies
115
views
R: problem with running time-series analysis software: Mfuzz
mfuzz
time-series
replace
15 hours ago by
soda
▴ 40
0
votes
0
replies
56
views
Running synteny of 2 strain.
Bioinformatics
19 hours ago by
jhilimsikder.biotech
• 0
0
votes
0
replies
62
views
statistical question (different number of gene orthologs on database)
database
statistics
20 hours ago by
v.berriosfarias
▴ 50
3
votes
3
replies
170
views
Lasso regression and cross-validation on RNA seq dataset
lasso
regression
rna-seq
cross-validation
updated 5 hours ago by
Mensur Dlakic
★ 18k • written 1 day ago by
Jipjop
▴ 10
3
votes
3
replies
196
views
SARS-CoV-2 lineages complete reference genomes
SARS-CoV-2
complete
genomes
reference
lineages
updated 1 day ago by
GenoMax
115k • written 1 day ago by
arash.iranzadeh1980
▴ 30
0
votes
2
replies
139
views
VCF file format for VCFTOOLs
plink
vcftools
vcf
updated 13 hours ago by
Pierre Lindenbaum
145k • written 1 day ago by
syxsu
• 0
7
votes
4
replies
224
views
Software to draw protein domains of proteins
Protein
domains
updated 1 day ago by
cmdcolin
★ 2.1k • written 1 day ago by
lukhanyomakhabane
▴ 10
1
vote
0
replies
79
views
How to calculate percentage of chimeras from r1/r2 files
chimera
usearch
chimeric
paired-end-reads
sequences
1 day ago by
eli_bayat
▴ 60
1
vote
2
replies
155
views
comparisons between 2 ChIP-seq datasets
ChIP-seq
8 hours ago by
Bogdan
★ 1.2k
0
votes
0
replies
112
views
NGS data analysis
tNGS
1 day ago by
bookorg
▴ 10
2
votes
1
reply
122
views
opern access database with vcf files for healthy people (controls)
VCF
database
controls
updated 1 day ago by
Jeremy
▴ 140 • written 2 days ago by
Liubov
▴ 20
0
votes
1
reply
116
views
RNA-seq Differential analysis general question of interpreting data results.
RNA-seq
Trininty
updated 1 day ago by
swbarnes2
12k • written 1 day ago by
lam.black.rider
• 0
2
votes
4
replies
205
views
MAF in R
Minor-Allele-Freq
R
MAF
1 day ago by
malgorzata.sobczak07
• 0
1
vote
1
reply
92
views
Making a pheatmap legend with superscripts
pheatmap
updated 1 day ago by
Ram
36k • written 1 day ago by
swbarnes2
12k
3
votes
7
replies
224
views
awk command help
Linux
shell-scripting
updated 1 day ago by
Pierre Lindenbaum
145k • written 1 day ago by
adyashapanda04
▴ 10
1
vote
2
replies
141
views
Why am I getting same linear regression lines for 'x' on 'y' and 'y' on 'x'?
lm
regression
linear
offtopic
updated 1 day ago by
karl.stamm
4.0k • written 1 day ago by
glyptonotus
• 0
1
vote
2
replies
157
views
Inflation in Imputed data
genomic
immunochip
inflation
topmed
1 day ago by
desicasares@gmail.com
▴ 10
1
vote
2
replies
144
views
Multi Alignment - How to deal with uncertainty?
alignment
transcriptomics
RNASeq
8 hours ago by
andrebolerbarros
• 0
1
vote
3
replies
149
views
How to deal with different transcripts ID between versions
gencode
ensembl
updated 1 day ago by
Ram
36k • written 1 day ago by
Manuel
• 0
0
votes
2
replies
126
views
Seurat cell cycle (single cell analysis)
single-cell
Seurat
cycle
1 day ago by
francesca3
▴ 70
1
vote
2
replies
163
views
bcftools error
genotype
error
vcf
ID
bcftools
1 day ago by
rheab1230
▴ 30
0
votes
0
replies
72
views
Mouse miRNA mapping
mirbase
mouse
alignment
bowtie
mirna
1 day ago by
AellSidious
• 0
2
votes
1
reply
109
views
Server Vendors to provide bioinformatics talents
vendor
updated 1 day ago by
GenoMax
115k • written 1 day ago by
Shicheng Guo
★ 9.0k
0
votes
0
replies
74
views
how to create a dataset from fastq sequence files in ubuntu
metagenomics
microbiome
dataset
usearch
ubuntu
1 day ago by
Flo
• 0
0
votes
0
replies
69
views
News:
In-person RNA-Seq Data Analysis Workshop in Leipzig, Germany (October 25-28, 2022)
Workshop
NGS
Transcriptomics
RNA-Seq
1 day ago by
David Langenberger
9.7k
2
votes
3
replies
191
views
How to filter out passed SNVs to create new files using bcftools isec.
isec
snv
1 day ago by
addamyeo
• 0
1
vote
2
replies
156
views
snakemake
pipeline
fastqc
snakemake
11 hours ago by
nishimalhotra2612
▴ 10
3
votes
4
replies
189
views
How to substract values in file in different colums from 1 ?
substraction
awk
1 day ago by
Akash Chandra Parida
▴ 40
0
votes
0
replies
79
views
C7 msigdb immune annotation results digging
annotation
Misgdb
RNA-Seq
1 day ago by
dew
• 0
2
votes
2
replies
206
views
Help with kallisto-bustools: how to interpret the inspect.json output file
pachter
scRNAseq
bustools
kallisto
updated 1 day ago by
dsull
★ 3.0k • written 1 day ago by
bompipi95
▴ 10
0
votes
0
replies
75
views
Best proteomics normalization for fold-change and pvalue calculation?
pvalue
proteomics
normalization
fold-change
1 day ago by
Doralicia
• 0
1
vote
6
replies
211
views
How to remove Duplicates in Sam file using AWK ?
protein
genome
gene
1 day ago by
sunnykevin97
▴ 540
0
votes
0
replies
216
views
[Error] The following command failed: perl P_aeruginosa_PAO1/cct_projects/dna_vs_dna/cgview_xml_builder.pl
CCT
updated 1 day ago by
rpolicastro
8.2k • written 1 day ago by
Neel
▴ 10
2
votes
9
replies
329
views
how to convert a protein sequence into a list of characters
python
list
updated 1 day ago by
Jeremy
▴ 140 • written 2 days ago by
Debut
▴ 40
4
votes
6
replies
717
views
bcftools merge of over 9000+ vcf files
vcf.gz
merge
bcftools
written 5 months ago by
Vanish007
▴ 10
0
votes
1
reply
104
views
Processing preanalyzed Bulk RNA sequencing data
visualization
preanalyzed
Bulk
RNA
data
Novogene
updated 1 day ago by
lieven.sterck
13k • written 1 day ago by
nils.simon.biology
• 0
8
votes
7
replies
276
views
Weird fastq quality distributions
fastq
distribution
updated 1 day ago by
GenoMax
115k • written 2 days ago by
evissc
▴ 30
101,924 results • Page
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Answer: How to regress out age and sex using limma removeBatchEffect
Answer: How to regress out age and sex using limma removeBatchEffect
How can I find a DNA sequence that codes for a protein from a large FASTQ file?
Answer: Server Vendors to provide bioinformatics talents
Comment: Weird fastq quality distributions
Answer: Server Vendors to provide bioinformatics talents
How to access the ACLAME server?
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Recent Replies
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴ 80
thank you, this worked. Appreciate your help so much.
Answer: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
cmdcolin
★ 2.1k
FASTQ files are generally raw reads, and you would not generally look for protein sequences from these raw reads. Possible reasons: short r…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴ 80
Will check that out. However, since this is proteomic expression, variance stabilized transformation is not the correct way to normalize th…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴ 80
Thank you for your help, I used covariates but was only able to regress out one variable. Will try the method you advised and also check co…
Comment: How to regress out age and sex using limma removeBatchEffect
by
linnaeusbundalian
• 0
Do you need the corrected assay? cause the removeBatchEffect affects only the assay for the visualization hence you need to extract it from…
Answer: How to regress out age and sex using limma removeBatchEffect
by
Gordon Smyth
★ 4.4k
You just use `removeBatchEffect` with `batch = sex`, `covariates = age` and `design = design`. Since you are already familiar with the `co…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴ 80
I tried that and it computes but I feel like its not correct because it is giving me many values of infinity. Is there a way to use the cov…
Comment: How to regress out age and sex using limma removeBatchEffect
by
aropri
▴ 80
so would first batch be batch = nph_csf_metadata$age, and second batch2 = nph_csf_metadata$sex?
Comment: How to access the ACLAME server?
by
GenoMax
115k
This appears to be a 10+ year old paper and as with many of these services it may be dead. Are you certain it was available recently?
Answer: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
GenoMax
115k
I will add one more idea. Once you get the DNA sequence of the protein you are looking for you can align (using a NGS data aligner) the rea…
Answer: How to regress out age and sex using limma removeBatchEffect
by
linnaeusbundalian
• 0
afaik, limma::removeBatchEffect can accept two batches i.e specifying batch = (first batch) and batch2 = (second batch)
Answer: How can I find a DNA sequence that codes for a protein from a large FASTQ file?
by
Mensur Dlakic
★ 18k
I think most people on this forum will tell you that you should solve your homeworks independently. That is the whole point of learning, an…
Comment: How to add the ancestral allele (AA) information in a vcf file?
by
Pierre Lindenbaum
145k
no, unless you have file similar to http://ftp.1000genomes.ebi.ac.uk/vol1/ftp/phase1/analysis_results/supporting/ancestral_alignments/
Comment: How to add the ancestral allele (AA) information in a vcf file?
by
taniamahmood38
▴ 20
Thanks for the help. But please kindly clarify that if the vcfancestralallele command will work on any specie vcf file other than human? …
Comment: Lasso regression and cross-validation on RNA seq dataset
by
Mensur Dlakic
★ 18k
Yes, the idea is to perform CV on a train dataset and evaluate on test. For this to be reliable, some kind of a stratified split is needed …
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