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370 results • Page
3 of 8
Sort: Votes
Rank
Views
Votes
Replies
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
2
votes
4
replies
2.2k
views
Negative values after batch correction using removeBatchEffect from Limma
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
2
votes
3
replies
341
views
Deseq2 : Paired analysis or otherwise
linear-regression
paired-analysis
DESeq2
longitudinal-analysis
updated 3 days ago by
ATpoint
81k • written 5 days ago by
IM
• 0
2
votes
6
replies
847
views
Batch effect correction with cell type enrichment analysis
limma
RNA-seq
r
batch-effect
updated 2 days ago by
Ram
43k • written 18 months ago by
JACKY
▴ 140
2
votes
1
reply
212
views
Trouble understanding seemingly contradicting results of GSE analysis (contradicting enriched GO terms with similar negative NES scores)
GSEA
pathways
GO-terms
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Manko47
• 0
2
votes
7
replies
592
views
Removing duplicates
duplicates
ONT
minimap2
updated 1 hour ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
2
votes
2
replies
1.1k
views
Can we directly use batch corrected gene expression (Bulk RNA-seq) for further downstream analyses?
RNA-Seq
batch-effect
updated 5 hours ago by
Ram
43k • written 5.0 years ago by
tigeradab
▴ 60
2
votes
2
replies
202
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
bgbs
• 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 5 hours ago by
Ram
43k • written 7.6 years ago by
gokce.ouz
▴ 70
2
votes
2
replies
881
views
Method to detect genome doubling
CNV
genome doubling
updated 1 day ago by
Zhenyu Zhang
★ 1.2k • written 4.4 years ago by
CY
▴ 750
2
votes
4
replies
324
views
Which command ro run MAKER pipeline for gene annotation ?
run.
command
to
MAKERpipeline.
updated 3 days ago by
GenoMax
141k • written 4 days ago by
Sony
▴ 10
2
votes
1
reply
2.3k
views
TCGA RNAseqV2 data matrix batch effect control and remove
RNA-Seq
batch-effect
updated 5 hours ago by
Ram
43k • written 7.6 years ago by
fractal61
▴ 10
2
votes
0
replies
184
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
3 days ago by
Alexander
▴ 220
2
votes
2
replies
1.0k
views
Batch correct batch 2 while leaving batch 1 unchanged.
limma
machine-learning
batch-effect
updated 6 hours ago by
Ram
43k • written 3.7 years ago by
i.sudbery
19k
2
votes
3
replies
1.5k
views
RNASeq - How to compare the expression of a single gene across batches
RNA-Seq
edgeR
batch-effect
updated 5 hours ago by
Ram
43k • written 3.5 years ago by
oakhamwolf
▴ 20
2
votes
2
replies
343
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 2 days ago by
Ram
43k • written 2 days ago by
Spring
• 0
2
votes
6
replies
489
views
Correcting coordinates in gff3 file
awk
unix
gff3
python
updated 6 days ago by
Matthias Zepper
4.5k • written 8 days ago by
hulu
• 0
2
votes
6
replies
5.1k
views
How to avoid over-correction by using harmony or CCA to batch correction in scRNA-seq?
scRNA-seq
R
seurat
harmony
batch-effect
updated 5 hours ago by
Ram
43k • written 3.7 years ago by
Lukadon77
• 0
2
votes
5
replies
332
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
1 day ago by
Bikram Kumar
• 0
2
votes
3
replies
235
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 2 days ago by
GenoMax
141k • written 2 days ago by
lorena9132
• 0
2
votes
4
replies
1.4k
views
How to fix Error in dat[, batch == batch_level] : (subscript) logical subscript too long when removing batch effects
microarray
combat
batch-effect
median-normalization
updated 6 hours ago by
Ram
43k • written 17 months ago by
Dominique
• 0
2
votes
3
replies
3.0k
views
RNA-seq batch effect correction
RNA-Seq
batch-effect
sequencing
updated 6 hours ago by
Ram
43k • written 6.9 years ago by
endikavarela
• 0
2
votes
2
replies
1.6k
views
How to add a title to a cnetplot?
r
cnetplot
updated 1 day ago by
Ram
43k • written 3.4 years ago by
appropiate
▴ 80
2
votes
2
replies
1.6k
views
Combining control samples from 2 separate studies. Model matrix for batch effect?
gene-expression
R
limma
batch-effect
model-matrix
updated 6 hours ago by
Ram
43k • written 7.2 years ago by
tolgaturant
▴ 20
2
votes
10
replies
3.4k
views
RepeatMasker: createLib() Error
RepeatMasker
updated 1 day ago by
Ram
43k • written 7.4 years ago by
linda
• 0
2
votes
2
replies
261
views
How to compare the quality of assemblies
nextdenovo
assembly
hifiasm
pacbio
updated 8 hours ago by
shelkmike
★ 1.2k • written 15 hours ago by
kirillkirilenko
▴ 30
2
votes
2
replies
328
views
differential gene expression analysis when not all samples have an untreated counterpart
differential-expression
edgeR
8 hours ago by
nhaus
▴ 300
2
votes
1
reply
235
views
VEP annotation --per_gene allele choice
VEP
updated 6 days ago by
Ram
43k • written 6 days ago by
atariw
▴ 10
2
votes
2
replies
241
views
How to row normalize a matrixplot?
scRNA-seq
RNA-seq
single-cell
scanpy
3 days ago by
bioinfo
▴ 150
2
votes
4
replies
262
views
SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by
kirill.zaslavsky
• 0
2
votes
1
reply
2.1k
views
How to make batch univariate cox analysis for list
univariate-cox-analysis
updated 9 hours ago by
Ram
43k • written 4.8 years ago by
BioLite
▴ 20
2
votes
3
replies
323
views
Sheep reference genome remapping coordinates
reference
remap
sheep
coordinates
genome
11 hours ago by
valentinatsar
• 0
2
votes
10
replies
559
views
Questions about a bug when transferring cram file to bam file
sequence
samtools
bcftools
updated 8 hours ago by
GenoMax
141k • written 1 day ago by
me
• 0
2
votes
1
reply
275
views
How to highlight genes on genome visual reprezentation/what tool to use?
gene
genome
updated 5 days ago by
Alex Reynolds
35k • written 5 days ago by
natami
▴ 10
2
votes
3
replies
925
views
Possible approach to select normal tissue samples for cancer RNA-Seq data without reference data for downstream analyses
R
RNA-Seq
DE
batch-effect
GTEx
updated 3 days ago by
Ram
43k • written 4.1 years ago by
svlachavas
▴ 790
2
votes
0
replies
1.8k
views
ComBat-seq adjustment of batch effects
RNA-Seq
ComBat-seq
SVA
edgeR
batch-effect
updated 1 day ago by
Ram
43k • written 3.4 years ago by
chatterjee.arumoy
▴ 50
2
votes
2
replies
943
views
Is there a file information dictionary for files downloaded from ENCODE through batch download?
ENCODE
updated 2 days ago by
Ram
43k • written 4.6 years ago by
burcakotlu
▴ 40
2
votes
5
replies
983
views
Ties in reranked list
fgsea
GSEA
updated 5 days ago by
Gordon
• 0 • written 6 months ago by
Hamza
• 0
2
votes
1
reply
3.1k
views
Batch effect correction in DE analysis of single cell RNA-seq data and visualization
Seurat
Batch-effect
SCDE
RNA-Seq
Limma
updated 1 day ago by
Ram
43k • written 5.5 years ago by
Poorya Parvizi
▴ 60
2
votes
3
replies
964
views
Treating "patient" as a batch effect
ComBat_seq
DESeq2
batch-Effect
updated 2 days ago by
Ram
43k • written 17 months ago by
Mia
▴ 20
2
votes
6
replies
3.6k
views
Algorithm to remove batch effects
single-cell
batch-effect
RNA-Seq
updated 2 days ago by
Ram
43k • written 3.3 years ago by
fouerghi20
▴ 80
2
votes
5
replies
2.8k
views
Batch effect in Axiom Human Origins Array
affymetrix
array
batch-effect
updated 2 days ago by
Ram
43k • written 7.9 years ago by
Simo
▴ 50
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 2 days ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
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 1 day ago by
Ram
43k • written 4.8 years ago by
asalimih
▴ 60
2
votes
2
replies
1.7k
views
Remove batch effect for many RNA-seq
ComBat
RNA-Seq
batch-effect
sva
updated 1 day ago by
Ram
43k • written 4.8 years ago by
Shaway
• 0
2
votes
4
replies
4.5k
views
Differential Expression Analysis with monocle and batch effect correction
single-cell
RNA-Seq
batch-effect
updated 1 day ago by
Ram
43k • written 5.9 years ago by
Poorya Parvizi
▴ 60
2
votes
2
replies
1.8k
views
Time point microarray data correcting for batch effects
microarray
combat
batch-effect
updated 6 hours ago by
Ram
43k • written 6.7 years ago by
tleona3
▴ 10
1
vote
2
replies
802
views
What type of normalization does removeBatchEffect function require as the input?
batch
limma
removeBatchEffect
rna-seq
batch-effect
updated 2 days ago by
Ram
43k • written 20 months ago by
ev97
▴ 20
1
vote
4
replies
373
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 5 days ago by
BioinfGuru
★ 1.7k • written 6 days ago by
Morteza
• 0
1
vote
1
reply
234
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 6 days ago by
Ram
43k • written 6 days ago by
Fish
• 0
370 results • Page
3 of 8
Recent Votes
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
Answer: Downloaded pdb's on rcsb.org
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Recent Replies
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.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
You can use the "Advanced query" builder (https://www.rcsb.org/search/advanced ) to create a query like: https://www.rcsb.org/search?requ…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
PDB has a search API: https://search.rcsb.org/#search-example-1 Here's the JSON from your search query: ``` { "query": { "type": "grou…
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
Thank you very much. Actually I looked at there, but actually I want to find something like according to search url like this [QUERY: Gene …
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