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Limit : this week
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337 results • Page
2 of 7
Sort: replies
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Views
Votes
Replies
2
votes
6
replies
843
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 1 day ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
1
vote
6
replies
1.6k
views
How can Differentially Expressed Genes be found by limma package after removing batch effect by ComBat function in sva package?
limma
sva
batch-effect
R
updated 2 days ago by
Ram
43k • written 3.8 years ago by
amirmehrgou
▴ 10
1
vote
6
replies
312
views
Rename multiple fastq.gz files
fastq
next-gen
updated 1 day ago by
shenwei356
8.4k • written 1 day ago by
Jérémie
• 0
4
votes
6
replies
3.9k
views
Correcting for batch effect in RNA-seq data
RNA-Seq
batch-effect
updated 8 hours ago by
Ram
43k • written 4.7 years ago by
Rimma
▴ 30
2
votes
6
replies
3.6k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 1 day ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
4
votes
6
replies
367
views
Odd results with BLAST remote
blast
remote
NCBI
updated 1 day ago by
b.contreras.moreira
▴ 150 • written 2 days ago by
Begonia_pavonina
▴ 150
8
votes
6
replies
2.5k
views
bwa 0.7.18 download to fix compile fail with GCC 10
bwa
updated 4 hours ago by
John Marshall
3.0k • written 23 months ago by
bioguy24
▴ 230
5
votes
6
replies
7.3k
views
scatter plot, aov()
aov
scatter-plot
anova
updated 20 hours ago by
Ram
43k • written 3.1 years ago by
Rob
▴ 170
0
votes
6
replies
498
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
2 days ago by
Dunois
★ 2.5k
2
votes
6
replies
421
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
6 days ago by
sansan_96
▴ 80
3
votes
6
replies
4.0k
views
Loading previously downloaded GEO SOfT data into R, using getGEO from GEOquery package
microarray
r
GEOquery
updated 20 hours ago by
Ram
43k • written 4.9 years ago by
mosesoo
▴ 30
3
votes
6
replies
2.4k
views
How to adjust by multiple variables using ComBat-Seq?
CombatSeq
combat
rna-seq
sva
batch-effect
updated 1 day ago by
Ram
43k • written 21 months ago by
ev97
▴ 20
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 2 days ago by
GenoMax
141k • written 14 months ago by
Estefania
▴ 30
15
votes
6
replies
1.2k
views
6 follow
VCF to human friendly form?
vcf
visualization
updated 2 days ago by
Pierre Lindenbaum
161k • written 19 months ago by
wormball
▴ 10
7
votes
6
replies
1.3k
views
using different microarray datasets (meta-analysis?) for DEG pipeline
microarray
meta-analysis
DEG
batch-effect
updated 8 hours ago by
Ram
43k • written 4.8 years ago by
mosesoo
▴ 30
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 1 day ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
3
votes
5
replies
1.3k
views
How to identify antibiotic resistant genes in gene databases?
antibiotic
Gene-Ontology
GO
updated 6 days ago by
Ram
43k • written 2.0 years ago by
ramin.k2013
• 0
0
votes
5
replies
2.0k
views
Batch effect correction & normalization after training/test split for gene expression data
RNA-seq
batch-effect
normalization
updated 1 day ago by
Ram
43k • written 20 months ago by
mmitra
▴ 60
1
vote
5
replies
1.5k
views
How to correct unknown Batch effect?
PCA
gene-expression
DESeq2
RNA-seq
batch-effect
updated 1 day ago by
Ram
43k • written 12 months ago by
luffy
▴ 110
4
votes
5
replies
3.4k
views
Please clarify me about countOverlaps()?
RNA-Seq
countOverlaps
R
updated 20 hours ago by
Ram
43k • written 6.3 years ago by
seta
★ 1.9k
1
vote
5
replies
305
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
2 days ago by
shpak.max
▴ 50
2
votes
5
replies
312
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
19 hours ago by
Bikram Kumar
• 0
1
vote
5
replies
2.3k
views
Shannon vs Simpson for TCR diversity estimation
TCR
shannon
simpson
updated 6 days ago by
ATpoint
81k • written 5.0 years ago by
CY
▴ 750
3
votes
5
replies
432
views
Having trouble building VG in Ubuntu
vg
updated 4 days ago by
Ram
43k • written 6 days ago by
ayushm64
• 0
1
vote
5
replies
2.8k
views
Batch effect identification using PCA
PCA
qRT-PCR
R
targeted-assay
Batch-Effect
updated 2 days ago by
Ram
43k • written 3.8 years ago by
mohammedtoufiq91
▴ 250
2
votes
5
replies
976
views
Ties in reranked list
fgsea
GSEA
updated 4 days ago by
Gordon
• 0 • written 6 months ago by
Hamza
• 0
0
votes
5
replies
290
views
Removing duplicates
duplicates
ONT
minimap2
updated 10 minutes ago by
joe
▴ 490 • written 14 hours ago by
quentinperriere
• 0
3
votes
5
replies
1.8k
views
Limma/edgeR Design matrix for gender effect
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 4.7 years ago by
kailsen
• 0
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 1 day ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
3
votes
5
replies
2.0k
views
DE analysis with edgeR and possibly batch effect
analysis
edgeR
batch-effect
DE
updated 8 hours ago by
Ram
43k • written 5.1 years ago by
seta
★ 1.9k
8
votes
5
replies
1.2k
views
Classifying repeat features from Ensembl
ensembl
repeat
updated 2 days ago by
e.r.zakiev
▴ 190 • written 15 months ago by
liorglic
★ 1.4k
1
vote
5
replies
318
views
samtools filtering
samtools
updated 6 days ago by
jkbonfield
★ 1.2k • written 14 days ago by
sansan_96
▴ 80
5
votes
5
replies
833
views
Blacklist for bacterial genome [ChIPseq]?
ChIPseq
Blacklist
updated 5 days ago by
Ram
43k • written 10 months ago by
Emily Wasson
▴ 30
2
votes
5
replies
1.9k
views
Differential Expression Analysis with batches which have different biological groups
R
RNA-Seq
limma
DE
batch-effect
updated 8 hours ago by
Ram
43k • written 4.8 years ago by
asalimih
▴ 60
0
votes
5
replies
449
views
Is it possible to set different tracks to the same scale in JBrowse
track
jbrowse
updated 5 days ago by
Ram
43k • written 7 days ago by
Jose
• 0
5
votes
5
replies
2.1k
views
batch effect in RNAseq analysis using tophat cufflinks pipeline
RNA-Seq
tophat
batch-effect
cufflinks
updated 8 hours ago by
Ram
43k • written 5.3 years ago by
yff
• 0
4
votes
4
replies
337
views
Bowtie2 mapping is slow
metagenomics
bowtie2
mapping
read
updated 5 days ago by
colindaven
6.3k • written 15 days ago by
Md Moinuddin
• 0
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 1 day ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
0
votes
4
replies
315
views
What is the samtools flag used in bamPEFragment?
deeptools
updated 6 days ago by
GenoMax
141k • written 8 days ago by
Soohyun
• 0
1
vote
4
replies
1.3k
views
Comparing RNA-Seq data to online databases
RNA-Seq
batch-effect
updated 21 hours ago by
Ram
43k • written 4.6 years ago by
Victoria
▴ 10
6
votes
4
replies
1.5k
views
RNA-Seq: X samples and X batches
RNA-Seq
edgeR
DESeq2
Batch-Effect
updated 21 hours ago by
Ram
43k • written 5.2 years ago by
Behram Radmanesh
▴ 40
4
votes
4
replies
2.6k
views
Advice on Handling Batch Effect in ChIP-seq Experiment
ChIP-Seq
batch-effect
sequencing
updated 8 hours ago by
Ram
43k • written 4.6 years ago by
dmj6ab
▴ 20
4
votes
4
replies
357
views
How do I install plink2 on a mac?
plink2
plink
updated 2 days ago by
zx8754
11k • written 5 days ago by
emilija.romic
▴ 10
1
vote
4
replies
355
views
Is it just me or has www.ensembl.org been broken for a while?
ensembl
6 days ago by
gene_biostars
• 0
2
votes
4
replies
232
views
SnpEff annotates coding duplication as intronic?
snpeff
20 hours ago by
kirill.zaslavsky
• 0
1
vote
4
replies
2.2k
views
Remove batch effect for prediction of RNA-seq data
RNA-Seq
batch-effect
Random-Forest
updated 8 hours ago by
Ram
43k • written 4.7 years ago by
Vlad
▴ 10
6
votes
4
replies
2.2k
views
Is there a way to get RNAFold output for multifasta in tabular format?
RNAFold
updated 13 hours ago by
jakobjung
• 0 • written 4.6 years ago by
adhirajnath14
▴ 40
3
votes
4
replies
345
views
How to download large-scale cDNA sequences from NCBI effectively ?
NCBI.
cDNA
updated 4 days ago by
Pierre Lindenbaum
161k • written 4 days ago by
Sony
▴ 10
3
votes
4
replies
3.3k
views
Motif analysis of DMRs (Differentially Methylated Regions) by HOMER
next-gen
updated 6 days ago by
Ram
43k • written 6.7 years ago by
inschigu
▴ 10
0
votes
4
replies
306
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
2 days ago by
pablo
▴ 300
337 results • Page
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High fold change values
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Prediction tools summary - zero values
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Error with Formatdb of legacy blast?
Answer: How to convert SAM/BAM file to GTF/GFF file?
A: Ribo-seq vs RNA-seq read count
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Recent Replies
Comment: Removing duplicates
by
joe
▴ 490
I *could* imagine an ONT scenario where you'd want to remove duplicates (amplicon-seq, etc) but likely for variant calling there is no need…
Comment: Removing duplicates
by
samuel.a.odonnell
▴ 510
As above, you do not need to worry about duplicates for ONT data Also have you looked at using other tools for variant calling more suited…
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by
geneontologyhelp
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If you're looking for the GO annotations for *Pediococcus acidilactici*, these are available. Using the instructions under [*2. All other…
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I just found an answer to this question here: [https://groups.google.com/g/cbioportal/c/hm_i4jbG1uc/m/h9rNYOvpAAAJ][1] [1]: https://gro…
Comment: Removing duplicates
by
joe
▴ 490
With ONT you will only have PCR duplicates. 'Read' (you mean optical?) duplicates are an artifact of cluster-based sequencing (ie Illumina)…
Comment: assembly using CCS, CLR, CCS_CLR sequences together?
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141k
PacBio has some recommendations on software for genome assemblies on this page (which you may have seen but just in case): https://www.pacb…
Answer: DEG analysis of RNA-seq data across multiple tissues and two conditions
by
swbarnes2
14k
I would not put totally different tissues in the same DESeq object. I don't think that's going to do good things for normalization or disp…
Comment: Removing duplicates
by
quentinperriere
• 0
pcr duplicates or/and read duplicates should I use this command to remove them ? or we don't talk about duplicates when dealing with ONT ??…
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If you didn't change the input signature matrix, the input RNA matrix, or the input parameters - what did you change? Is the statement that…
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Your best option may be to email the author (and/or the senior author from the paper). Let them know that the FTP links mentioned on GitHub…
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Thanks @lchart, I accept that, I'll wait to see if there's any more who want to input and then accept the answer
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What kind of data is this? Plain genomic/amplicons? How you proceed will largely depend on the context. Can you also post the original fast…
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by
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▴ 510
I guess the enlightening question is: duplicates of what?
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by
LChart
3.9k
I don't think this approach will give you what you want. Combining multiple tissues in the way you are suggesting will result in a positive…
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