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158 results • Page
2 of 4
Sort: Views
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Views
Votes
Replies
0
votes
3
replies
1.1k
views
Batch effect for SNP array
sva
combat
batch-effect
SNP
updated 3 days ago by
Ram
43k • written 4.2 years ago by
Taylor95
▴ 10
0
votes
0
replies
1.1k
views
Should batch correction be performed before or after feature selection in scRNA-seq
batch-effect
scRNA-seq
feature-selection
updated 1 day ago by
Ram
43k • written 4.9 years ago by
Lucy
▴ 140
0
votes
0
replies
1.1k
views
Finding wobble/redundant positions in an RNA string using R.
RNA
wobble-position
R
updated 1 day ago by
Ram
43k • written 6.2 years ago by
fawazfebin
▴ 100
0
votes
2
replies
1.0k
views
proportional hazard assumption was not satisfied for a covariate
hazard-ratios
Cox-model
survival
updated 1 day ago by
Ram
43k • written 4.3 years ago by
akutasame
▴ 40
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
0
votes
0
replies
881
views
Advice on group specific condition effect and model matrix in deseq2
deseq2
batch-effect
updated 3 days ago by
Ram
43k • written 4.1 years ago by
Mozart
▴ 330
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
0
votes
0
replies
832
views
Estimating sequence complexity of DNA sequence from fasta file
sequence
RepeatMasker
pacbio
updated 1 day ago by
Ram
43k • written 5.6 years ago by
epaminonda
▴ 10
0
votes
1
reply
825
views
How to compare differentially expressed genes among different affymatrix dataset
microarray
batch-effect
R
updated 1 day ago by
Ram
43k • written 4.8 years ago by
Calangoa
▴ 30
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
0
votes
1
reply
794
views
Bulk RNAseq MACS Sort Quality Contamination
EdgeR
Batch-effect
RNA-Seq
updated 4 hours ago by
Ram
43k • written 3.7 years ago by
jordan15
• 0
4
votes
13
replies
757
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 1 day ago by
BioinfGuru
★ 1.7k • written 7 days ago by
matteo.levorato
• 0
0
votes
0
replies
724
views
"No group or design set" with deAna() function in EnrichmentBrowser package
RNA-Seq
R
EnrichmentBrowser
updated 1 day ago by
Ram
43k • written 4.1 years ago by
yxswhx
• 0
0
votes
0
replies
713
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
RNA-Seq
scRNA-Seq
batch-effect
updated 4 hours ago by
Ram
43k • written 3.4 years ago by
hkarakurt
▴ 180
1
vote
0
replies
662
views
Conditions for valid batch effect correction
r
batch-effect
updated 1 day ago by
Ram
43k • written 5.1 years ago by
Sebastian Hesse
▴ 340
1
vote
1
reply
652
views
Save experiment with batch effects - Protein microarray
statistics
protein-array
batch-effect
updated 1 day ago by
Ram
43k • written 4.3 years ago by
s.lima.diogenes
▴ 10
8
votes
10
replies
651
views
bash script
whole-genome-sequencing
updated 3 days ago by
Ram
43k • written 10 days ago by
bestone
▴ 30
2
votes
2
replies
625
views
Batch correction for DE analysis
batch-correction
mRNA
RNA-seq
DEGs
MDSplot
updated 1 day ago by
Ram
43k • written 2.6 years ago by
Yoonji
▴ 10
2
votes
7
replies
581
views
Removing duplicates
duplicates
ONT
minimap2
updated 10 minutes ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
0
votes
9
replies
544
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 6 days ago by
LauferVA
4.2k • written 8 days ago by
Aki
▴ 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
0
votes
6
replies
510
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
3 days ago by
Dunois
★ 2.5k
0
votes
2
replies
503
views
autodockvina
python
python3
autodock
updated 2 hours ago by
Ram
43k • written 3 months ago by
iamsmor
• 0
0
votes
4
replies
396
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
16 hours ago by
feather-W
• 0
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
0
votes
1
reply
359
views
How to add rowLinks, rowTree in SummarizedExperiment manually.
phylogenetic-tree
microbiome
updated 8 hours ago by
Ram
43k • written 19 months ago by
Muhammad
• 0
0
votes
3
replies
339
views
Per base sequence content failed miserably
fastqc
sequence
trimmomatic
NGS
assembly
updated 4 hours ago by
GenoMax
141k • written 1 day ago by
Kai Xin
• 0
2
votes
5
replies
331
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
0
votes
4
replies
315
views
Compute bootstrap values on consensus tree
phylogeny
tree
raxml
3 days ago by
pablo
▴ 300
1
vote
3
replies
304
views
Ensembl gene id conversion
biomart
ensembl
updated 2 days ago by
ATpoint
81k • written 4 days ago by
naveedhasan2000
• 0
0
votes
3
replies
297
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 5 days ago by
ATpoint
81k • written 7 days ago by
gdfsnkfns
• 0
0
votes
2
replies
297
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
5 days ago by
O.rka
▴ 710
1
vote
2
replies
287
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 3 days ago by
Istvan Albert
100k • written 4 days ago by
Jiang
• 0
0
votes
2
replies
281
views
How can I solve this error?
metal
20 hours ago by
22211020193
• 0
0
votes
2
replies
268
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 6 days ago by
Zhenyu Zhang
★ 1.2k • written 6 days ago by
Apollonia
• 0
0
votes
2
replies
261
views
GSEA analysis in R
GSEA
R
Arabidopsis
14 hours ago by
Sudip
• 0
2
votes
4
replies
261
views
SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by
kirill.zaslavsky
• 0
0
votes
2
replies
257
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
2 days ago by
Koketso
• 0
1
vote
2
replies
256
views
Tumour purity and ploidy estimation
Copy-number
Whole-exome-sequencing
2 days ago by
bp22
▴ 60
0
votes
2
replies
254
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
6 days ago by
ramin.k2013
• 0
3
votes
1
reply
254
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 6 days ago by
Ram
43k • written 7 days ago by
rj.rezwan
• 0
1
vote
3
replies
253
views
True variants selection
vcf
bcftools
updated 6 days ago by
dthorbur
★ 1.9k • written 7 days ago by
maevalefeuvre
• 0
0
votes
2
replies
247
views
WGCNA
PCA
WGCNA
EIGENGENE
6 days ago by
rajasekargutha
▴ 60
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
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
0
votes
2
replies
234
views
RNAseq 1 control 2 different treatment
RNA-seq
2 days ago by
matteo.levorato
• 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
0
votes
1
reply
230
views
How to get the reference panel for UKBB
UKBB
GWAS
clump
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
航太郎
• 0
1
vote
2
replies
229
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
2 days ago by
bioinfo
▴ 150
0
votes
2
replies
228
views
How to identify gaps in a genome?
awk
seqkit
assembly
fasta
genome
3 days ago by
rj.rezwan
• 0
158 results • Page
2 of 4
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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