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121,398 results • Page
1 of 2428
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Votes
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0
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0
replies
15
views
DESeq2 LRT test with multifactorial design
test
design
multifactorial
LRT
49 minutes ago by
lessismore
★ 1.4k
0
votes
0
replies
24
views
Scvi - Integration
integration
singlecell
scvi
2 hours ago by
t.foskolos
• 0
0
votes
0
replies
35
views
Genotype Imputations Question
vcf
imputations
genomics
4 hours ago by
Jonathan
• 0
0
votes
1
reply
78
views
Clarification of options --keep-dup: all vs. -f FRAG in MACS3
human
libraries
illumina
callpeak
macs3
updated 8 hours ago by
ATpoint
88k • written 8 hours ago by
María José
▴ 10
5
votes
2
replies
339
views
Should I perform integration to correct batch effects?
batch
effect
updated 12 hours ago by
antonioggsousa
3.3k • written 4 days ago by
han
▴ 20
840
votes
170
replies
180k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 7 weeks ago by
Biostar
3.6k • written 8.5 years ago by
Istvan Albert
102k
2
votes
1
reply
96
views
Batch correction in TNBC epithelial cells
tnbc
seurat
epithelialCells
scRNAseq
BatchEffect
updated 13 hours ago by
ATpoint
88k • written 14 hours ago by
TNF_alpha
• 0
2
votes
5
replies
313
views
7 follow
Best way to install R packages on an HPC?
R
HPC
updated 20 hours ago by
Charles Plessy
★ 2.9k • written 1 day ago by
ChumBucket2024
▴ 10
0
votes
1
reply
84
views
how to use filter_vep to filter vcf file
vcf
filter
updated 16 minutes ago by
Jeremy Leipzig
23k • written 22 hours ago by
htchd
• 0
0
votes
2
replies
138
views
How to interpret genomescope to help remove duplicates
assembly
hifi
genomescope
23 hours ago by
mohamadelian1996
• 0
0
votes
2
replies
140
views
Is it valid to stack brightfield and fluorescence channels in a CNN input?
fluorescent-microscopy
imaging
microscopy
updated 1 day ago by
LChart
5.0k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
76
views
FusionCatcher cases where gene1 and gene 2 have 2 matches
fusions
fusioncatcher
1 day ago by
ieie
▴ 20
0
votes
2
replies
135
views
mgl tool index error
docking
molecular
error
14 hours ago by
Mahesh
• 0
2
votes
3
replies
215
views
convert raw counts to TPM
R
updated 1 day ago by
dthorbur
★ 3.0k • written 1 day ago by
pinheirofabiano
▴ 130
1
vote
7
replies
234
views
Creating kraken2 custom database
kraken2
updated 1 day ago by
GenoMax
152k • written 1 day ago by
ramiro.barrantes
▴ 60
0
votes
0
replies
81
views
How to determine the coordinate of the transposon insertion on the reverse reading?
Tn-seq
transposon
blastn
1 day ago by
Елизавета
• 0
0
votes
5
replies
229
views
Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
Alevin-Fry
single-cell
sequencing
Salmon
RNA
updated 6 hours ago by
Rob
7.1k • written 1 day ago by
wooh
• 0
0
votes
0
replies
87
views
News:
Conservation Genomics course
PopulationGenomics
Ne
ConservationGenomics
1 day ago by
Physalia-courses
★ 2.6k
0
votes
3
replies
218
views
Snakemake Module Error: string indices must be integers
GATK
Snakemake
updated 1 day ago by
Jesse
▴ 870 • written 1 day ago by
andean
• 0
1
vote
3
replies
215
views
How do I generate a Manhattan plot like this?
data-visualization
manhattan-plot
1 day ago by
jianhua.mert
• 0
0
votes
2
replies
226
views
ATAC seq: from peaks to differential analysis ??
MACS2
DESeq2
ATACseq
updated 1 day ago by
rfran010
★ 1.5k • written 2 days ago by
Picasa
▴ 680
1
vote
1
reply
163
views
Where to find expected copy number for a gene
genomics
updated 1 day ago by
GenoMax
152k • written 2 days ago by
LayneSadler
▴ 90
0
votes
4
replies
1.1k
views
Cut&Run replicates handling
peakcaller
replicates
SEACR
chipseq
updated 2 days ago by
schowdhury8950
• 0 • written 12 months ago by
g.anande
• 0
0
votes
1
reply
151
views
Unable to extract count matrices from multi-layered Seurat object
seurat
2 days ago by
bgbs
• 0
17
votes
12
replies
580
views
7 follow
Learning Nextflow
Genomic
Pipeline_analysis
Nextflow
2 days ago by
AIMAR
▴ 20
3
votes
1
reply
245
views
open target platform SNP to Gene qurey
SNPtoGene
GWAS
SNP
updated 3 days ago by
GenoMax
152k • written 3 days ago by
SeoG
▴ 10
0
votes
1
reply
219
views
usage of ChromHMM and Segway
ChromHMM
Segway
updated 2 days ago by
Pierre Lindenbaum
166k • written 3 days ago by
qian
• 0
2
votes
6
replies
2.0k
views
Which tools do you recommend me use to get the maximum information of a protein?
protein
software
updated 3 days ago by
fileyfood
▴ 20 • written 8.7 years ago by
Hamtaro
▴ 60
8
votes
4
replies
1.5k
views
Tools for predicting protein function?
protein
updated 3 days ago by
fileyfood
▴ 20 • written 4.1 years ago by
jamie.pike
▴ 90
8
votes
12
replies
2.8k
views
Map genome positions onto protein coordinates?
pdb
protein
variant
updated 3 days ago by
fileyfood
▴ 20 • written 20 months ago by
cmdcolin
★ 4.2k
3
votes
3
replies
1.4k
views
Online tool for creating figures of gene with its features
features
genes
figures
updated 3 days ago by
fileyfood
▴ 20 • written 2.6 years ago by
andre.arrudalima
▴ 80
2
votes
5
replies
1.4k
views
Simple tools for creation of figures of gene and protein structure
gene
protein
updated 3 days ago by
fileyfood
▴ 20 • written 19 months ago by
andre.arrudalima
▴ 80
5
votes
3
replies
1.3k
views
To create amino acid substitution in protein structure
protein
software
updated 3 days ago by
fileyfood
▴ 20 • written 4.2 years ago by
shwetamgr1
▴ 20
40
votes
12
replies
12k
views
13 follow
Where Can I Get The Secondary Structure Of A Protein?
protein
structure
sequence
updated 3 days ago by
fileyfood
▴ 20 • written 15.4 years ago by
Giovanni M Dall'Olio
28k
5
votes
2
replies
2.2k
views
Database Of Structurally Derived Protein Features
uniprot
database
updated 3 days ago by
fileyfood
▴ 20 • written 11.2 years ago by
samesense
▴ 50
2
votes
3
replies
1.8k
views
Protein structure and snps
gene
SNP
updated 3 days ago by
fileyfood
▴ 20 • written 8.8 years ago by
H.Hasani
★ 1.0k
14
votes
7
replies
11k
views
Modelling Effect Of Mutation On Protein Structure
protein
protein
mutation
updated 3 days ago by
fileyfood
▴ 20 • written 13.3 years ago by
didymos
▴ 220
1
vote
2
replies
1.1k
views
Comparison of protein structures
protein
updated 3 days ago by
fileyfood
▴ 20 • written 7.7 years ago by
lochanamp
▴ 80
3
votes
3
replies
4.1k
views
Tools to display mutations in a protein's structure
protein
sequence
updated 3 days ago by
fileyfood
▴ 20 • written 9.3 years ago by
sviatoslav.kendall
▴ 980
2
votes
12
replies
687
views
Different comparisons in RNASeq Analysis
DEGs
RNAseq
updated 13 hours ago by
mbyvcm
▴ 460 • written 5 days ago by
SomeOne
▴ 200
0
votes
1
reply
271
views
Querying on non-canonical bacterial IDs
microbes
protein
accession
updated 5 days ago by
Mensur Dlakic
★ 29k • written 5 days ago by
benjamin.kellman
• 0
0
votes
4
replies
406
views
Distribution of assayed SNPs per sample
distribution
PLINK
missingness
3 days ago by
am29
▴ 60
0
votes
0
replies
237
views
News:
Learn Python for Biological Data Analysis – Online Course this September!
NGS
Python
Programming
5 days ago by
Physalia-courses
★ 2.6k
3
votes
0
replies
268
views
Tutorial:
How to calculate partial correlation controlling cancer types
CRISPR
biology
correlation
computational
bioinformatics
5 days ago by
Ming Tommy Tang
★ 4.7k
0
votes
1
reply
298
views
SAIGE-GENE error
R
SAIGE
updated 6 days ago by
GenoMax
152k • written 6 days ago by
smyiz
▴ 30
2
votes
1
reply
1.3k
views
IGV track display problem: interval rectangle from BED file appears above all tracks in white, overlapping each other
IGV
bed
6 days ago by
mcsimenc
▴ 30
2
votes
2
replies
359
views
Y-axis break in Volcano Plot
Volcano_Plot
Enhanced_Volcano
updated 7 hours ago by
antonioggsousa
3.3k • written 6 days ago by
rajdeepboral00
▴ 70
1
vote
0
replies
276
views
How to rank a gene list using correlation coefficient and p-values for GSEA/clusterProfiler?
ClusterProfiler
GSEA
correlation
rank
genelist
6 days ago by
c-wes
▴ 10
5
votes
4
replies
497
views
Nanopore data analysis
nanopore
updated 6 days ago by
colindaven
7.6k • written 6 days ago by
sarahmanderni
▴ 130
6
votes
2
replies
1.6k
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 6 days ago by
ashotmarg2004
▴ 130 • written 21 months ago by
a615ebfb
▴ 50
121,398 results • Page
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Answer: Should I perform integration to correct batch effects?
is there a tool to recover corrupted fastq files
Answer: is there a tool to recover corrupted fastq files
Answer: Questions about a bug when transferring cram file to bam file
Answer: When should I NOT apply batch correction for my single-cell RNAseq data?
Answer: Should I perform integration to correct batch effects?
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★ 3.0k
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Recent Replies
Comment: how to use filter_vep to filter vcf file
by
Jeremy Leipzig
23k
are these VCFs derived from transcripts? why would an intron be missing from a genomic VCF?
Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
by
Rob
7.1k
The main issue is that there will be an inherent lack of information (due to the aforementioned 3' bias) in tagged-end data. Nonetheless, …
Comment: Y-axis break in Volcano Plot
by
antonioggsousa
3.3k
I am not familiar with the package `EnhancedVolcano`, but based on your code, should not you be able to change the y-axis limits through th…
Answer: Clarification of options --keep-dup: all vs. -f FRAG in MACS3
by
ATpoint
88k
As per the manual, `FRAG` is specific for scATAC-seq while the other option is generic.
Answer: Should I perform integration to correct batch effects?
by
antonioggsousa
3.3k
Hi, Please check my previous answer to a similar post/question on this forum: [When should I NOT apply batch correction for my single-cel…
Answer: Batch correction in TNBC epithelial cells
by
ATpoint
88k
> (1) Is my pipeline correct? Especially re-applying the harmony to the sub-setted the TNBC epithelial cells. You **can** do that. No prob…
Comment: Different comparisons in RNASeq Analysis
by
mbyvcm
▴ 460
My suggestion is that you consider performing what is commonly referred to as a "delta-delta" contrast. You should be able to find plenty o…
Comment: mgl tool index error
by
Mahesh
• 0
no i am simply drag and drop my pdbqt file in GUI
Answer: Best way to install R packages on an HPC?
by
Charles Plessy
★ 2.9k
At my workplace I created a Singularity image that has most of the C/C++ libraries installed, and R's library path pointing to an image-spe…
Comment: Best way to install R packages on an HPC?
by
cfos4698
★ 1.1k
FWIW, I've recently still been running into environment solving issues with conda (even with the incorporated libmamba changes) that mamba …
Comment: How to interpret genomescope to help remove duplicates
by
mohamadelian1996
• 0
Thank you for helping me out. Other related species have genomes ranging between 400 and 700 Mb so the length given here by genomescope see…
Comment: How to interpret genomescope to help remove duplicates
by
GenoMax
152k
What is the expected genome size and ploidy for this organism? Can you post the busco results?
Comment: Is it valid to stack brightfield and fluorescence channels in a CNN input?
by
LChart
5.0k
Not a real answer, but it should be pointed out that the only way to learn contrastive filters across modalities (i.e., fluorescence-only e…
Answer: Is it valid to stack brightfield and fluorescence channels in a CNN input?
by
Mensur Dlakic
★ 29k
I think this is a borderline bioinformatics question, but I'll still attempt to answer. You won't break the computer by merging all three …
Comment: mgl tool index error
by
GenoMax
152k
Are you using command line or some sort of GUI? Post the full command if you are doing this on the command line.
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