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121,411 results • Page
1 of 2429
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0
votes
0
replies
13
views
mm10 blacklist regions detailed information
sequencing
DNA
blacklist
1 hour ago by
annaA
▴ 10
0
votes
1
reply
37
views
identify unmapped regions
human
illumina
libraries
updated 2 hours ago by
GenoMax
152k • written 2 hours ago by
María José
▴ 10
0
votes
1
reply
65
views
martCheck - Error - You must provide a valid Mart object - for running HoneyBADGER for CNV computation
CNV
biomaRt
HoneyBADGER
4 hours ago by
mete.han.celebi
• 0
0
votes
1
reply
66
views
How to Specify Power Parameter for Adjacency in modulePreservation() (WGCNA)
module
analysis
WGCNA
preservation
updated 5 hours ago by
andres.firrincieli
3.9k • written 6 hours ago by
Berkan
• 0
0
votes
1
reply
75
views
filters used in mutation discovery from RNAseq data
filter
RNAseq
mutation
updated 3 hours ago by
GenoMax
152k • written 12 hours ago by
htchd
▴ 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
3
replies
197
views
Trouble Using GEO Files with Seurat
seurat
GEO
scRNA
14 hours ago by
Jamie
• 0
0
votes
0
replies
77
views
Knowledge Graph for AI
KnowledgeGraph
biotech
AI
SPOKE
Bioinformatician
20 hours ago by
Cornelio
• 0
2
votes
2
replies
815
views
How to convert from .spec to .bam?
bam
file-formatting
spec
updated 21 hours ago by
Daniel Lai
▴ 10 • written 4.7 years ago by
gmora
▴ 30
2
votes
1
reply
119
views
Insert size is zero
rna-seq
fastp
insert
size
updated 21 hours ago by
GenoMax
152k • written 22 hours ago by
SpliceAndScript
• 0
0
votes
3
replies
197
views
Should matched samples (not paired) be included in the DESeq2 design model?
edgeR
limma
DESeq2
updated 7 hours ago by
i.sudbery
21k • written 1 day ago by
marieke
• 0
0
votes
4
replies
192
views
Trajectory Analysis scRNA-seq with one cell type and two developmental stages
cellrank
palantir
pseudotime-trajectory-analysis
scrna-seq
trajectory-analysis
8 hours ago by
npont
▴ 10
0
votes
1
reply
486
views
How to run trajectory analysis with only one cell type using palantir?
palantir
scanpy
updated 1 day ago by
npont
▴ 10 • written 11 months ago by
bioinfo
▴ 160
0
votes
0
replies
77
views
should I remove the transcripts from annotate peak region in ATAC-seq
ATAC-seq
1 day ago by
QX
▴ 70
3
votes
2
replies
189
views
DESeq2 LRT test with multifactorial design
test
design
multifactorial
LRT
1 day ago by
lessismore
★ 1.4k
1
vote
0
replies
446
views
Tool:
Created a better alternative to clunky gene databases, with functions that are consolidated from various gene databases. It's your one-stop shop for …
browser
export
data
search
gene
1 day ago by
Krish
• 0
1
vote
0
replies
110
views
Tool:
Containerized NGS Data Processing Pipelines
rna-seq
atac-seq
pipeline
chip-seq
docker
1 day ago by
Noah
▴ 10
0
votes
1
reply
135
views
Scvi - Integration
integration
singlecell
scvi
updated 1 day ago by
antonioggsousa
3.3k • written 1 day ago by
t.foskolos
• 0
0
votes
0
replies
111
views
Genotype Imputations Question
vcf
imputations
genomics
2 days ago by
Jonathan
• 0
0
votes
1
reply
150
views
Clarification of options --keep-dup: all vs. -f FRAG in MACS3
human
libraries
illumina
callpeak
macs3
updated 2 days ago by
ATpoint
88k • written 2 days ago by
María José
▴ 10
6
votes
2
replies
440
views
Should I perform integration to correct batch effects?
batch
effect
updated 2 days ago by
antonioggsousa
3.3k • written 6 days ago by
han
▴ 20
2
votes
1
reply
169
views
Batch correction in TNBC epithelial cells
tnbc
seurat
epithelialCells
scRNAseq
BatchEffect
updated 2 days ago by
ATpoint
88k • written 2 days ago by
TNF_alpha
• 0
2
votes
5
replies
401
views
7 follow
Best way to install R packages on an HPC?
R
HPC
updated 2 days ago by
Charles Plessy
★ 2.9k • written 3 days ago by
ChumBucket2024
▴ 10
2
votes
2
replies
211
views
how to use filter_vep to filter vcf file
vcf
filter
1 day ago by
htchd
▴ 20
1
vote
2
replies
211
views
How to interpret genomescope to help remove duplicates
assembly
hifi
genomescope
2 days ago by
mohamadelian1996
• 0
0
votes
2
replies
200
views
Is it valid to stack brightfield and fluorescence channels in a CNN input?
fluorescent-microscopy
imaging
microscopy
updated 2 days ago by
LChart
5.0k • written 2 days ago by
Antonio
• 0
0
votes
0
replies
130
views
FusionCatcher cases where gene1 and gene 2 have 2 matches
fusions
fusioncatcher
3 days ago by
ieie
▴ 20
0
votes
2
replies
209
views
mgl tool index error
docking
molecular
error
2 days ago by
Mahesh
• 0
2
votes
3
replies
299
views
convert raw counts to TPM
R
updated 3 days ago by
dthorbur
★ 3.0k • written 3 days ago by
pinheirofabiano
▴ 130
1
vote
7
replies
334
views
Creating kraken2 custom database
kraken2
updated 3 days ago by
GenoMax
152k • written 3 days ago by
ramiro.barrantes
▴ 60
0
votes
0
replies
136
views
How to determine the coordinate of the transposon insertion on the reverse reading?
Tn-seq
transposon
blastn
3 days ago by
Елизавета
• 0
0
votes
6
replies
343
views
Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
Alevin-Fry
single-cell
sequencing
Salmon
RNA
7 hours ago by
wooh
• 0
0
votes
0
replies
139
views
News:
Conservation Genomics course
PopulationGenomics
Ne
ConservationGenomics
3 days ago by
Physalia-courses
★ 2.6k
0
votes
3
replies
273
views
Snakemake Module Error: string indices must be integers
GATK
Snakemake
updated 2 days ago by
Jesse
▴ 870 • written 3 days ago by
andean
• 0
1
vote
3
replies
281
views
How do I generate a Manhattan plot like this?
data-visualization
manhattan-plot
3 days ago by
jianhua.mert
• 0
0
votes
2
replies
284
views
ATAC seq: from peaks to differential analysis ??
MACS2
DESeq2
ATACseq
updated 3 days ago by
rfran010
★ 1.5k • written 4 days ago by
Picasa
▴ 680
1
vote
1
reply
216
views
Where to find expected copy number for a gene
genomics
updated 3 days ago by
GenoMax
152k • written 3 days ago by
LayneSadler
▴ 90
0
votes
4
replies
1.1k
views
Cut&Run replicates handling
peakcaller
replicates
SEACR
chipseq
updated 3 days ago by
schowdhury8950
• 0 • written 12 months ago by
g.anande
• 0
0
votes
1
reply
206
views
Unable to extract count matrices from multi-layered Seurat object
seurat
3 days ago by
bgbs
• 0
21
votes
12
replies
683
views
7 follow
Learning Nextflow
Genomic
Pipeline_analysis
Nextflow
4 days ago by
AIMAR
▴ 40
3
votes
1
reply
295
views
open target platform SNP to Gene qurey
SNPtoGene
GWAS
SNP
updated 5 days ago by
GenoMax
152k • written 5 days ago by
SeoG
▴ 10
0
votes
1
reply
282
views
usage of ChromHMM and Segway
ChromHMM
Segway
updated 4 days ago by
Pierre Lindenbaum
166k • written 5 days ago by
qian
• 0
2
votes
6
replies
2.1k
views
Which tools do you recommend me use to get the maximum information of a protein?
protein
software
updated 5 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 5 days ago by
fileyfood
▴ 20 • written 4.1 years ago by
jamie.pike
▴ 90
8
votes
12
replies
2.9k
views
Map genome positions onto protein coordinates?
pdb
protein
variant
updated 5 days ago by
fileyfood
▴ 20 • written 20 months ago by
cmdcolin
★ 4.2k
3
votes
3
replies
1.5k
views
Online tool for creating figures of gene with its features
features
genes
figures
updated 5 days ago by
fileyfood
▴ 20 • written 2.6 years ago by
andre.arrudalima
▴ 80
2
votes
7
replies
1.5k
views
6 follow
Simple tools for creation of figures of gene and protein structure
gene
protein
updated 1 day ago by
Krish
• 0 • written 19 months ago by
andre.arrudalima
▴ 80
5
votes
3
replies
1.4k
views
To create amino acid substitution in protein structure
protein
software
updated 5 days ago by
fileyfood
▴ 20 • written 4.2 years ago by
shwetamgr1
▴ 20
40
votes
13
replies
12k
views
14 follow
Where Can I Get The Secondary Structure Of A Protein?
protein
structure
sequence
updated 1 day ago by
Krish
• 0 • 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 5 days ago by
fileyfood
▴ 20 • written 11.2 years ago by
samesense
▴ 50
121,411 results • Page
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Comment: Distribution of assayed SNPs per sample
Comment: How to convert from .spec to .bam?
Comment: making psam file for plink2
A: GSVA on RNAseq data (GTEX)
GSVA on RNAseq data (GTEX)
A: GSVA kernels: Gaussian or Poisson?
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Comment: identify unmapped regions
by
GenoMax
152k
> We've created a coverage file of the aligments against the GRCh38 reference genome Are you referring to regions that are hard to align r…
Comment: filters used in mutation discovery from RNAseq data
by
GenoMax
152k
One line questions are never a good way to describe what you are trying to do and without that information you are not likely to get any us…
Answer: martCheck - Error - You must provide a valid Mart object - for running HoneyBADG
by
mete.han.celebi
• 0
Hello everyone, I have fixed the issue. Here how I fixed: mart.obj <- useMart( biomart = "ENSEMBL_MART_ENSEMBL", da…
Answer: How to Specify Power Parameter for Adjacency in modulePreservation() (WGCNA)
by
andres.firrincieli
3.9k
multiData can contain your adjacency matrices. Then in `modulePreservation()` set `dataIsExpr = FALSE`
Comment: Should matched samples (not paired) be included in the DESeq2 design model?
by
i.sudbery
21k
No thats not what I mean. When you run DESeq, if fits values to each of the coeffients that you specify. You then compute p-values on som…
Comment: Single-cell RNA Sequencing - transcript abundance estimation using Alevin-Fry
by
wooh
• 0
Thank you that makes sense. When previously doing this it seemed the quantification result had assigned exact equal values of two transcrip…
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
by
npont
▴ 10
Yes I would agree for clustering, but the way I define my cell type is not based on clustering: I define cells as being of my type of inter…
Comment: Should matched samples (not paired) be included in the DESeq2 design model?
by
marieke
• 0
Ah yes, looking at the PCA makes sense, thanks! I'm not sure I understand your last paragraph, though. With 'running tests', do you mean r…
Comment: Trouble Using GEO Files with Seurat
by
Jamie
• 0
Thank you so much @antonioggsousa! You've helped me a lot!
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
by
Bastien Hervé
6.4k
It makes sense to me to give it a try like this, however along the way depending on your batch effect correction or your pseudotime sanity …
Answer: Insert size is zero
by
GenoMax
152k
It is possible, if your have libraries that failed and are just adapter dimers. You could also try `bbmerge.sh` from BBMap suite to get a…
Comment: How to convert from .spec to .bam?
by
Daniel Lai
▴ 10
https://github.com/molonc/spec-1.3.2
Comment: Trouble Using GEO Files with Seurat
by
1769mkc
★ 1.3k
merge and the scanpy anndata.concat are they doing exactly same?
Comment: Trajectory Analysis scRNA-seq with one cell type and two developmental stages
by
npont
▴ 10
Hello, Thank you for your reply Indeed visium HD goes down to 2um resolution but I applied a nuclei segmentation which worked pretty nicel…
Answer: Should matched samples (not paired) be included in the DESeq2 design model?
by
i.sudbery
21k
You add an extra covariate to the design matrix when you expect that it will explain some of the variance in gene expression. In general, i…
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