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1,000 results • Page
6 of 20
Sort: replies
Rank
Views
Votes
Replies
1
vote
5
replies
562
views
Duplicate marking, read names, and the SRA
SRA
MarkDuplicates
updated 7 days ago by
GenoMax
141k • written 7 days ago by
Luka
• 0
0
votes
5
replies
5.9k
views
Calculate Radius of Gyration [python 3]
biopython
PDB
Radius of Gyration
python
protein
updated 7 days ago by
ndm1096
• 0 • written 6.5 years ago by
ac.research
▴ 30
1
vote
5
replies
1.5k
views
Blastn in galaxy
Blastn
galaxy
updated 24 days ago by
Ram
43k • written 3.0 years ago by
adnan.lahuf
• 0
0
votes
5
replies
493
views
Is it possible to set different tracks to the same scale in JBrowse
track
jbrowse
updated 14 days ago by
Ram
43k • written 16 days ago by
Jose
• 0
3
votes
5
replies
2.1k
views
DE analysis with edgeR and possibly batch effect
analysis
edgeR
batch-effect
DE
updated 9 days ago by
Ram
43k • written 5.1 years ago by
seta
★ 1.9k
2
votes
5
replies
1.6k
views
Adding functional annotation and meta-data of MAKER/BRAKER GFF
metadata
functional-annotation
BRAKER
MAKER
updated 25 days ago by
andorjkiss
▴ 40 • written 15 months ago by
javanokendo
▴ 60
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 9 days ago by
Ram
43k • written 5.9 years ago by
Poorya Parvizi
▴ 60
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 10 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
4
replies
2.0k
views
Requesting help with RNA-Seq differential gene analysis
differential-gene-expression
deseq2
updated 17 days ago by
Ram
43k • written 6.2 years ago by
sagnik
▴ 50
4
votes
4
replies
14k
views
Heatmap with custom gene labels annotated on the rows
differential-gene-expression
RNAseq
heatmap
updated 17 days ago by
Ram
43k • written 4.7 years ago by
bioinforesearchquestions
▴ 370
1
vote
4
replies
365
views
Molecular docking with Autodock
Docking
proteomics
updated 21 days ago by
Ram
43k • written 12 weeks ago by
shwetamgr1
▴ 10
2
votes
4
replies
320
views
SnpEff annotates coding duplication as intronic?
snpeff
10 days ago by
kirill.zaslavsky
• 0
2
votes
4
replies
1.2k
views
PLINK p value returning NA
GWAS
PLINK
updated 18 days ago by
chrchang523
10k • written 18 months ago by
Sin Yu, Lin
• 0
2
votes
4
replies
2.4k
views
How could I generate a gi_taxid_nucl.dmp file similar to the one previously hosted by NCBI?
ncbi
metagenomics
centrifuge
gi_taxid_nucl.dmp
taxonomy
updated 2 days ago by
ZhangYuanfeng
• 0 • written 2.4 years ago by
Frazier Baker
• 0
2
votes
4
replies
318
views
Number of CPUs to use by DRAP for transcriptomic assmbly
DRAP
CPU
transcriptomics
28 days ago by
Mohamed Abderrahmane
▴ 20
2
votes
4
replies
312
views
What is the real meaning of relative enrichment/peak height of ChIP-seq tracks?
ChIP-seq
3 days ago by
HyperEvo
• 0
3
votes
4
replies
310
views
Tutorial:
how to combine multiple RNAseq count files into a single dataframe in R and unix
Unix
RNAseq
R
updated 10 minutes ago by
BioinfGuru
★ 1.7k • written 2 days ago by
Ming Tommy Tang
★ 3.9k
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 10 days ago by
Ram
43k • written 2.9 years ago by
Sib
▴ 60
1
vote
4
replies
3.1k
views
remove batch effect for multiple tumor data
RNA-Seq
batch-effect
updated 8 days ago by
Ram
43k • written 7.1 years ago by
hellocita
▴ 40
3
votes
4
replies
3.5k
views
any recommended tools for batch effect and normalization not written in R?
R
RNA-Seq
combat
python
batch-effect
updated 8 days ago by
Ram
43k • written 7.1 years ago by
dyollluap
▴ 310
0
votes
4
replies
818
views
Differential gene expression
limma
differential-gene-expression
R
updated 17 days ago by
Ram
43k • written 4.0 years ago by
innyus
▴ 40
1
vote
4
replies
373
views
Homer giving troubles
homer
HOMER
19 days ago by
naveedhasan2000
• 0
1
vote
4
replies
396
views
Is it just me or has www.ensembl.org been broken for a while?
ensembl
15 days ago by
gene_biostars
• 0
0
votes
4
replies
1.2k
views
Batch effects
Batch-effect
transcriptomics
updated 8 days ago by
Ram
43k • written 2.6 years ago by
BioQueen
▴ 30
4
votes
4
replies
364
views
Average expression of a sample in single-cell data
single-cell
rna-seq
24 days ago by
newuser2024
• 0
1
vote
4
replies
1.4k
views
Removing/Accounting for batch effects in unbalanced group RNAseq data
rna-seq
batch-effect
deseq
updated 8 days ago by
Ram
43k • written 2.2 years ago by
claysandel
• 0
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq
batch-effect
updated 10 days ago by
Ram
43k • written 4.7 years ago by
Victoria
▴ 10
1
vote
4
replies
346
views
How to get human-mouse conservation score from UCSC
conservation
mouse
IGV
human
score
21 days ago by
diqixiaoyaoer
▴ 10
0
votes
4
replies
334
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 16 days ago by
GenoMax
141k • written 18 days ago by
Soohyun
• 0
7
votes
4
replies
1.4k
views
Is there any journal article to reference removeBatchEffect function from Limma?
batch
removebatcheffect
limma
rna-seq
batch-effect
updated 10 days ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
0
votes
4
replies
505
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
9 days ago by
feather-W
• 0
0
votes
4
replies
6.5k
views
fastq-dump: command not found, what is wrong?
assembly
sratoolkit
genomics
updated 24 days ago by
spalmer
• 0 • written 2.7 years ago by
BioinfoNoob6
• 0
0
votes
4
replies
277
views
Adaptive sampling for whole chromosomes
T2T
Nanopore
AdaptiveSampling
aneuploidy
centromeres
16 days ago by
njornet
▴ 20
2
votes
4
replies
373
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 12 days ago by
GenoMax
141k • written 12 days ago by
Sony
▴ 10
2
votes
4
replies
2.6k
views
DESeq2 inconsistent results
differential-gene-expression
RNA-Seq
DESeq2
updated 17 days ago by
Ram
43k • written 8.1 years ago by
Chris Gene
▴ 80
1
vote
4
replies
268
views
cloupe to 10x format
seurat
10X
cloupe
updated 22 days ago by
Ram
43k • written 23 days ago by
M'zelle
• 0
12
votes
4
replies
2.3k
views
long read + salmon? (transcript abundance)
long-read
salmon
updated 21 days ago by
Ram
43k • written 14 months ago by
shinyjj
▴ 50
2
votes
4
replies
421
views
chromHMM annotations
chromHMM
19 days ago by
nswati106
• 0
2
votes
4
replies
6.0k
views
Batch Effect Removal in RNA-Seq Data for DGE & WGCNA. Should I omit any samples according to PCA plots?
Batch-effect
RNA-Seq
R
DESeq2
updated 8 days ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
1
vote
4
replies
2.8k
views
removing confounding batch effect with RUVseq
RUVseq
RNA-Seq
batch-effect
DESeq2
updated 9 days ago by
Ram
43k • written 5.1 years ago by
grant.hovhannisyan
★ 2.6k
1
vote
4
replies
280
views
Removing batch effect using combat-seq
batch
effect
RNA-Seq
combat-seq
updated 25 days ago by
BioinfGuru
★ 1.7k • written 26 days ago by
Netanel
• 0
0
votes
4
replies
429
views
How evaluate assembly when multiple reference strains are available?
Genome
Quast
Reference
Assembly
updated 25 days ago by
dthorbur
★ 1.9k • written 28 days ago by
MetaPaul
• 0
0
votes
4
replies
580
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
8 days ago by
Kai Xin
• 0
4
votes
4
replies
401
views
How do I install plink2 on a mac?
plink2
plink
updated 12 days ago by
zx8754
11k • written 14 days ago by
emilija.romic
▴ 10
1
vote
4
replies
2.4k
views
Batch effect control in GWAS data.
Batch-effect
omniexpress
GWAS
GSA
updated 9 days ago by
Ram
43k • written 4.8 years ago by
saksis.rihards
▴ 10
3
votes
4
replies
430
views
biomaRt error for different R version
biomaRt
R
updated 9 days ago by
GenoMax
141k • written 10 days ago by
manaswwm
▴ 490
2
votes
4
replies
303
views
Should I use unpaired reads from trimmomatic
RNA-seq
QC
Trimmomatic
updated 3 days ago by
swbarnes2
14k • written 4 days ago by
dxj294
• 0
9
votes
4
replies
1.9k
views
Integration of RNA-Seq data with microarray data
microarray
RNA-Seq
batch-effect
R
updated 10 days ago by
Ram
43k • written 4.0 years ago by
Fahimeh.6868
▴ 30
3
votes
4
replies
663
views
Mapping cDNA sequence of a single gene to a genome not hosted at UCSC server (without Blat)
mapping
4 days ago by
rahu
• 0
0
votes
4
replies
524
views
how to find genes that are significantly expressed in brain cortex samples
rna-seq
gene-expression
updated 6 days ago by
ATpoint
82k • written 7 days ago by
rheab1230
▴ 140
1,000 results • Page
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Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
BioinfGuru
★ 1.7k
Thanks Ram
Comment: ScRNA data question
by
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▴ 10
features <- SelectIntegrationFeatures(object.list = merged_dat) data.anchors <- FindIntegrationAnchors(object.list = merged_dat, …
Comment: gvcf joint calling
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• 0
Thank you for your help! I really appreciate it! And you know, the merged WES gVCF files still have "NA" loci. For such cases, I am quite …
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https://maayanlab.cloud/clustergrammer/ It's a web-based tool (can also be a python jupyter widget) that I find useful for exploring a pat…
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There is an Agilent array case study in the limma User's Guide, which you might find helpful and somewhat simpler. I don't recommend col…
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Gordon Smyth
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The comparison you've done seems exactly right to test whether treatment 2 modifies or enhances the effect of treatment 1. Have you exam…
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There's no need for form a contrast because the score variable is already in the model. A continuous variable is its own contrast. Just run…
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Oh wow, bedops closest-features, how did I overlook that!! I didn't know about it; thank you! Your awk script is beautiful. This worked per…
Comment: Create a new bed file with all pairwise combinations between two other bed files
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J
▴ 10
Thank you Pierre! I'll try this out with my full data set.
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I happend to see one paper doing the similar thing, share it with you guys, "A systematic evaluation of normalization methods and probe rep…
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I think Pierre's answer might be correct for your test input, but it doesn't account for the start position of the reference element and so…
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You need to be clear about how `Seurat` defines highly variable genes here. Highly variable genes are the genes that have very high express…
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141k
Please include a link when you are recommending a tool. There can be programs with similar names.
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