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366 results • Page
2 of 8
Sort: Votes
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Views
Votes
Replies
5
votes
2
replies
1.7k
views
Batch effects from sequencing samples accross multiple flow cells.
rna-seq
batch
batch-effect
sequencing
updated 2 days ago by
Ram
43k • written 2.9 years ago by
Mat
▴ 60
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 1 day ago by
Ram
43k • written 3.1 years ago by
Rob
▴ 170
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 1 day ago by
Ram
43k • written 5.3 years ago by
yff
• 0
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
Rimma
▴ 30
4
votes
13
replies
759
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 2 days ago by
BioinfGuru
★ 1.7k • written 7 days ago by
matteo.levorato
• 0
4
votes
0
replies
161
views
Herald:
The Biostar Herald for Monday, April 15, 2024
herald
3 days ago by
Biostar
2.6k
4
votes
6
replies
1.4k
views
CompressedGRangesList don't have seqLengths: BiocParallel errors: Error in covRleFromGR(x, weight = weight, ignore.strand = ignore.strand): Seqlength…
gff3
GenomicRanges
ORFik
GenomicFeatures
updated 3 days ago by
GenoMax
141k • written 14 months ago by
Estefania
▴ 30
4
votes
4
replies
342
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 6 days ago by
colindaven
6.3k • written 16 days ago by
Md Moinuddin
• 0
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 1 day ago by
Ram
43k • written 4.6 years ago by
dmj6ab
▴ 20
4
votes
3
replies
2.2k
views
The result of differential gene expression analysis should be extracted based on adj.p.value ?
limma
microarray
bioconductor
R
updated 1 day ago by
Ram
43k • written 6.3 years ago by
Raheleh
▴ 260
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 1 day ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
4
votes
4
replies
366
views
How do I install plink2 on a mac?
plink2
plink
updated 3 days ago by
zx8754
11k • written 6 days ago by
emilija.romic
▴ 10
4
votes
7
replies
4.5k
views
snakemake output directory
snakemake
ngs
updated 2 days ago by
进
• 0 • written 3.9 years ago by
Peter Chung
▴ 200
4
votes
6
replies
386
views
Odd results with BLAST remote
blast
remote
NCBI
updated 2 days ago by
b.contreras.moreira
▴ 150 • written 3 days ago by
Begonia_pavonina
▴ 150
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 1 day ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
4
votes
2
replies
3.7k
views
DESeq2 design and batch effect
RNA-Seq
batch-effect
DESeq2
Salmon
updated 10 hours ago by
Ram
43k • written 6.5 years ago by
georgewwp
▴ 30
4
votes
2
replies
243
views
Assume "yes" as the answer to any prompts with bioconda
docker
container
bioconda
updated 17 hours ago by
Juke34
8.5k • written 18 hours ago by
njornet
▴ 20
4
votes
4
replies
443
views
Why number of interactions decreased in current string database for plasmodium
string
interactions
ppi
updated 6 days ago by
damian.szk
▴ 50 • written 7 days ago by
rohitsatyam102
▴ 840
4
votes
2
replies
232
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 2 days ago by
Ram
43k • written 2 days ago by
Adi
▴ 10
4
votes
7
replies
524
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 5 days ago by
Ram
43k • written 6 days ago by
AHerik
▴ 20
4
votes
10
replies
1.5k
views
Do I have batch effect?
RNA-Seq
edgeR
batch-effect
updated 3 days ago by
Ram
43k • written 3.9 years ago by
avino
▴ 20
3
votes
10
replies
574
views
Piping samtools to R
R
NGS
bash
samtools
2 days ago by
joe
▴ 500
3
votes
4
replies
350
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 5 days ago by
Pierre Lindenbaum
161k • written 5 days ago by
Sony
▴ 10
3
votes
3
replies
375
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
2 days ago by
ayushm64
• 0
3
votes
8
replies
4.9k
views
An idea to identify batch effects
microarray
batch-effect
updated 10 hours ago by
Ram
43k • written 9.6 years ago by
mjarosz
• 0
3
votes
1
reply
6.1k
views
Normalization before or after merging the samples in Seurat
single-cell
seurat
batch-effect
updated 2 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
3
votes
3
replies
3.0k
views
Quick way to Identify batch effect from covariates?
bioconductor
batch-effect
updated 10 hours ago by
Ram
43k • written 7.9 years ago by
James Ashmore
★ 3.4k
3
votes
7
replies
1.0k
views
Can I use batch effect correction "by parts"?
ComBat
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 4.3 years ago by
n,n
▴ 360
3
votes
2
replies
1.2k
views
DESeq2 design and Batch effects
RNA-Seq
batch-effect
DESeq2
updated 1 day ago by
Ram
43k • written 4.4 years ago by
baldissera152
▴ 10
3
votes
8
replies
4.1k
views
Using FPKM and TPM values for batch correction for Single Cell RNA-Seq
fpkm
scRNA-seq
RNA-Seq
tpm
batch-effect
updated 10 hours ago by
Ram
43k • written 4.5 years ago by
hkarakurt
▴ 180
3
votes
6
replies
879
views
Any problem re-using last year's RNA-Seq data in this year's analysis?
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 3.7 years ago by
oakhamwolf
▴ 20
3
votes
2
replies
4.1k
views
Batch effects in sequencing data
batch-effect
updated 10 hours ago by
Ram
43k • written 8.7 years ago by
Andrew
▴ 60
3
votes
4
replies
335
views
biomaRt error for different R version
biomaRt
R
updated 16 hours ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
3
votes
11
replies
5.9k
views
Modifying R pairs() function
plotMEpairs
WGCNA
R
updated 1 day ago by
Ram
43k • written 6.4 years ago by
shania90.lk
▴ 30
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 2 days ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
3
votes
2
replies
802
views
Retrieve initial query in getBM()
getBM
biomaRt
R
gene
updated 1 day ago by
Ram
43k • written 3.1 years ago by
helia.ziaei
• 0
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 2 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 1 day ago by
Ram
43k • written 5.0 years ago by
mosesoo
▴ 30
3
votes
2
replies
2.1k
views
Batch effect correction - miRNA sequencing - DESeq2
Batch-effect
DESeq2
miRNA-Seq
updated 2 days ago by
Ram
43k • written 5.4 years ago by
prekrish
• 0
3
votes
5
replies
442
views
Having trouble building VG in Ubuntu
vg
updated 5 days ago by
Ram
43k • written 7 days ago by
ayushm64
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 2 days ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
3
votes
7
replies
376
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
2 days ago by
ntsopoul
▴ 60
3
votes
1
reply
559
views
What is the normalization status of metabric data?
metabric
normalization
microarray
cbioportal
updated 1 day ago by
etiennedanis
▴ 20 • written 19 months ago by
DareDevil
★ 4.3k
3
votes
6
replies
8.3k
views
RNA-seq, EdgeR and batch effects
RNA-Seq
removeBatchEffect
edgeR
batch-effect
updated 2 days ago by
Ram
43k • written 9.3 years ago by
Ekarl2
▴ 120
3
votes
4
replies
3.8k
views
Error in ComBat function: Error in dat[, batch == batch_level] : (subscript) logical subscript too long
Batch-effect
microarray
R
updated 2 days ago by
Ram
43k • written 2.8 years ago by
Sib
▴ 60
3
votes
2
replies
1.0k
views
Can I take 'organ type' as a batch effect and use ComBat to remove organ dependent variations?
RNA-Seq
Cross-Species
SVA
ComBat
Batch-Effect
updated 2 days ago by
Ram
43k • written 4.6 years ago by
rodguinea
• 0
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis
edgeR
batch-effect
DE
updated 1 day ago by
Ram
43k • written 5.1 years ago by
seta
★ 1.9k
3
votes
4
replies
3.4k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 10 hours ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
3
votes
3
replies
265
views
Korean human genome reference file
GWAS
reference
imputation
33 minutes ago by
SeoGyun
• 0
366 results • Page
2 of 8
Recent Votes
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: Korean human genome reference file
by
SeoGyun
• 0
Thanks..... But I want to do imputation, so I have to make it as a vcf file, but the site only has a fatsa file....
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
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