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121,170 results • Page
1 of 2424
Sort: Rank
Rank
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Votes
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0
votes
1
reply
19
views
Single cell expression and accessibility integration using cellxgene data
cellxgene
updated 40 minutes ago by
GenoMax
151k • written 51 minutes ago by
1769mkc
★ 1.3k
0
votes
1
reply
124
views
Umbrella pathways in KEGG
KEGG
R
updated 2 hours ago by
Arup Ghosh
3.3k • written 1 day ago by
Arindam Ghosh
▴ 540
0
votes
2
replies
59
views
Peptide protein dynamics
Pepdide
updated 48 minutes ago by
lieven.sterck
15k • written 2 hours ago by
venkatramananspd
• 0
1
vote
0
replies
41
views
Alternatives to WGCNA
WGCNA
3 hours ago by
Poorvi
▴ 10
0
votes
1
reply
50
views
variant calling chromosome-wise from WGS data
wgs
updated 20 minutes ago by
cmdcolin
★ 4.2k • written 4 hours ago by
analyst
▴ 60
5
votes
5
replies
158
views
Design matrix with uneven patient representation across stages
RNA-seq
design-matrix
limma
2 hours ago by
Lucas
• 0
1
vote
2
replies
106
views
Forum:
The best LLM or any tool to generate legal regex expression string for specific usage?
regex
awk
sed
commands
linux
updated 5 hours ago by
GenoMax
151k • written 7 hours ago by
JustinZhang
▴ 140
0
votes
0
replies
47
views
Question about vg giraffe, vg surject and Visualization tool for mapping result
vg
8 hours ago by
gulin
• 0
2
votes
6
replies
2.0k
views
6 follow
minimap2 gets killed, but it doesn't explain why
minimap2
updated 2 hours ago by
Arup Ghosh
3.3k • written 14 months ago by
michael.flower.14
▴ 200
837
votes
170
replies
176k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 15 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
0
replies
55
views
Reference-guided transcriptome assembly using multiple SRA experiments ?
assembly
Transcriptome
projects
SRA
8 hours ago by
debitboro
▴ 270
2
votes
4
replies
150
views
Heatmap of a transformed deseq object with pheatmap
deseq2
pheatmap
41 minutes ago by
caroline.zanchi
• 0
5
votes
10
replies
2.7k
views
Minimap2 error in Flye de novo assembly
Flye
Minimap2
10 hours ago by
Nilo
▴ 10
0
votes
0
replies
58
views
How to find hormone related proteins from a list of gene/proteins
R
bioinformatics
12 hours ago by
WUSCHEL
▴ 860
0
votes
0
replies
69
views
mtDNA variants from WGS data
mitogenome
recovery
data
from
WGS
14 hours ago by
wonde2000
• 0
0
votes
0
replies
66
views
Using structure prediction approaches to predict interaction between two proteins
protein
prediction
structure
18 hours ago by
Daniel
▴ 30
0
votes
1
reply
109
views
Merge 1000 Genome gentotype AND genotype likelihood VCFs together
VCF
LiftoverVcf
Merge
updated 18 hours ago by
Giulio Genovese
▴ 630 • written 19 hours ago by
JourneyToAbyss
▴ 240
0
votes
0
replies
79
views
Writing genepop from genind
R
genepop
genind
graph4lg
stacks
21 hours ago by
eaabbott0
• 0
3
votes
4
replies
1.9k
views
Remove all entries with duplicate names from fastq file?
fastq
illumina
duplicate
updated 22 hours ago by
Charles-Alexandre Roy
▴ 50 • written 3.9 years ago by
wormball
▴ 10
1
vote
1
reply
111
views
Copy Number Variants with CNVKit
CVNs
Somatic_variant
Recommendations
CNVKit
updated 21 hours ago by
GenoMax
151k • written 23 hours ago by
AIMAR
• 0
0
votes
0
replies
86
views
Basecount calculation after alignment to multi-fasta file
multi-fasta
sequence
bwa
consensus
samtool
alignment
1 day ago by
aj
• 0
0
votes
0
replies
89
views
TEtranscripts analysis
TEtranscripts
1 day ago by
frarodmar17
• 0
0
votes
0
replies
92
views
CVNkit call commande
CVNs
CNVKit
Somatic_variant
23 hours ago by
AIMAR
• 0
0
votes
3
replies
159
views
FraserDataSet() error in FRASER
R
splicing
FRASER
RNAseq
alternative
updated 2 hours ago by
marco.barr
▴ 170 • written 1 day ago by
n_navy
• 0
0
votes
1
reply
145
views
Strange volcano - DEGs with p.adj=0 look weird
RNA-seq
DEGs
updated 7 hours ago by
manaswwm
▴ 570 • written 1 day ago by
noodlejackson
▴ 40
2
votes
3
replies
409
views
What is the difference between JASPAR IDs MA0668.3 and MA1993.2 for Neurod2?
motifs
atac-seq
factor
jaspar
transcription
updated 1 day ago by
GenoMax
151k • written 11 days ago by
Ambuj
• 0
0
votes
0
replies
91
views
News:
Online course: Introduction to R and Bioconductor
R
Bioconductor
Genomics
1 day ago by
Physalia-courses
★ 2.6k
0
votes
0
replies
92
views
IM-fusion data analysis
IM-fusion
1 day ago by
frarodmar17
• 0
0
votes
3
replies
182
views
error in reading codelink data
readcodelinkset
error
updated 2 hours ago by
marco.barr
▴ 170 • written 1 day ago by
nazaninhoseinkhan
▴ 530
0
votes
1
reply
158
views
DiffBind analysis with ENCODE data using R and .bed/.bam files
R
ChIP-seq
ENCODE
Diffbind
updated 1 day ago by
Aspire
▴ 380 • written 1 day ago by
stalo.lili
• 0
7
votes
5
replies
611
views
No variant in the Pseudoautosomal regions of gomad chrY ?
chrY
PAR
vcf
gnomad
Pseudoautosomal
updated 21 hours ago by
cmdcolin
★ 4.2k • written 16 days ago by
Pierre Lindenbaum
166k
8
votes
6
replies
3.3k
views
News:
Boston Ma Us Area Folks: Software Carpentry Workshop For Women In Science Coming Up
python
training
updated 1 day ago by
GenoMax
151k • written 12.1 years ago by
Mary
11k
1
vote
1
reply
233
views
Selecting clinical rows for repeated case IDs in TCGA-BRCA data
Clinical-Data
Breast-Cancer
TCGA
updated 1 day ago by
Zhenyu Zhang
★ 1.3k • written 3 days ago by
BhagyashreeWaghale
• 0
0
votes
2
replies
259
views
Kallisto to tximport to deseq2
enseml
deseq2
Kallisto
updated 2 days ago by
GenoMax
151k • written 2 days ago by
bioinfo
▴ 150
0
votes
1
reply
226
views
Pooling Replicates in Omics Analysis: Trade-off Between Cost and Data Robustness?
Replicates
Omics
Pooling
updated 2 days ago by
ATpoint
88k • written 3 days ago by
sardius
• 0
0
votes
0
replies
150
views
Tool for Estimation of Purity and Ploidy in Precancerous Lesions
CNV
purity
genome
ploidy
3 days ago by
ting
• 0
9
votes
8
replies
672
views
6 follow
Nextflow: split a FASTA file into 5 parts to enable parallel processing
nextflow
workflow
pipeline
3 days ago by
neng
▴ 40
0
votes
1
reply
214
views
What to choose as background in statistic test genetics
test
expression
gene
statistic
updated 2 days ago by
Dunois
★ 2.9k • written 3 days ago by
adigershon8897
• 0
5
votes
4
replies
448
views
differential exon usage from Salmon outputs
edgeR
diffSpliceDGE
DEU
salmon
updated 3 days ago by
Gordon Smyth
★ 8.0k • written 6 days ago by
n_navy
• 0
0
votes
0
replies
275
views
Multi-SNP Behavioral and Frequency Profile Inquiry: TPH2, GRM2, COMT, DRD2, HTR1A (Rare Interaction)
population-genetics
genetic-variation
epistasis
snp
gnomad
3 days ago by
SonicSoal
• 0
0
votes
0
replies
167
views
Rare variants association analysis (using WGS)
variant
GWAS
rare
WGS
3 days ago by
SeoG
• 0
0
votes
0
replies
177
views
Convert AnnData to Seurat (spatial transcriptomics, visium HD)
seurat
segmentation
anndata
visiumhd
updated 3 days ago by
GenoMax
151k • written 3 days ago by
npont
• 0
0
votes
0
replies
182
views
News:
Online course -Reproducibility in Bioinformatics - July 7–9
Singularity
Git
Docker
Snakemake
Nextflow
4 days ago by
Physalia-courses
★ 2.6k
1
vote
5
replies
453
views
RNA-Sequencing Analysis when control samples paired-end and tumour samples single-end
ENA
rna-sequencing
4 days ago by
h
• 0
0
votes
3
replies
341
views
STAR aligner - how is quality and correctness tested across builds/releases?
STAR
updated 4 days ago by
GenoMax
151k • written 4 days ago by
Arthur
• 0
1
vote
2
replies
326
views
Pathway enrichment analysis on time-series data by filtering out age comparisons
pea
go
rnaseq
time-series
4 days ago by
fullycratered
• 0
6
votes
8
replies
498
views
building snpeff database for plant
plant
updated 7 hours ago by
lieven.sterck
15k • written 4 days ago by
analyst
▴ 60
1
vote
1
reply
241
views
How to find motif in specific region
motif
chip-seq
updated 4 days ago by
Alex Reynolds
36k • written 4 days ago by
zhang616123
• 0
0
votes
0
replies
220
views
How to interpret perplexing qcovhsp result in blastx
blastx
qcovhsp
blastn
3 days ago by
samuel.himes
• 0
0
votes
0
replies
193
views
Representation of GT:DS INFO tag for a missing marker in a VCF file
VCF
bcftools
4 days ago by
Mwangana
• 0
121,170 results • Page
1 of 2424
Recent Votes
Comment: Are there mm39/GRCm39 blacklist regions?
Comment: Are there mm39/GRCm39 blacklist regions?
Are there mm39/GRCm39 blacklist regions?
Are there mm39/GRCm39 blacklist regions?
Answer: Heatmap of a transformed deseq object with pheatmap
Answer: Heatmap of a transformed deseq object with pheatmap
A: bwa-mem: [bam_sort_core] merging from 0 files and 3 in-memory blocks
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Recent Replies
Comment: variant calling chromosome-wise from WGS data
by
cmdcolin
★ 4.2k
I'm not experienced with this type of problem, but you may be able to get some coarse-level understanding of the plody by just looking at a…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
Thank you very much ! Yes I guess I should center and scale. I am always uneasy about doing this, but this would make everything more reada…
Comment: Heatmap of a transformed deseq object with pheatmap
by
caroline.zanchi
• 0
I think you very very much for your help. It worked. I think I will have to take off the legend and add it separately though, because I am …
Comment: Single cell expression and accessibility integration using cellxgene data
by
ATpoint
88k
Would you mind formatting your wall of code with markdown? thank you.
Comment: Peptide protein dynamics
by
lieven.sterck
15k
much better, thanks :-)
Comment: Design matrix with uneven patient representation across stages
by
Lucas
• 0
Thank you!
Comment: error in reading codelink data
by
marco.barr
▴ 170
Sure, I have sent you an email to your institutional account.
Comment: Peptide protein dynamics
by
lieven.sterck
15k
welcome to the forum https://www.biostars.org/u/150315/ , unfortunately this kind of question phrasing will not get you much response. D…
Comment: FraserDataSet() error in FRASER
by
marco.barr
▴ 170
Not having full insight into the structure of a FRASER object, I wrote the code I thought might work. You can try making the rownames uniq…
Answer: Umbrella pathways in KEGG
by
Arup Ghosh
3.3k
If you are interested in the hierarchical terms, they can be found in the KEGG BRITE database. Web: https://www.kegg.jp/brite/ko0000…
Comment: FraserDataSet() error in FRASER
by
n_navy
• 0
Thank you for reply. When I run the first option, nothing's changed, same error occured. However, in second option this error occured; …
Comment: Design matrix with uneven patient representation across stages
by
GenoMax
151k
Moving this answer to a comment since it seems to contradict answer provided by @gordonsmyth (author of edgeR).
Comment: The best LLM or any tool to generate legal regex expression string for specific
by
GenoMax
151k
Can you provide an example of something that you have tried that did not work? Perhaps it is matter of the question you ask and how you ask…
Answer: Design matrix with uneven patient representation across stages
by
Gordon Smyth
★ 8.0k
Uneven patient representation is handled in limma/edgeR by treating patient as a random effect. For RNA-seq, you would use ``` library(edge…
Comment: Seurat3: RNA vs SCT assays for DotPlot
by
txema.heredia
▴ 210
Apologies for resurrecting this old post. When googling about "Seurat FindAllMarkers SCTransform" I have seen suggested on many forums tha…
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