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121,384 results • Page
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News:
Conservation Genomics course
PopulationGenomics
Ne
ConservationGenomics
1 hour ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
104
views
Snakemake Module Error: string indices must be integers
GATK
Snakemake
4 hours ago by
andean
• 0
0
votes
2
replies
63
views
Best way to install R packages on an HPC?
R
HPC
updated 17 minutes ago by
QX
▴ 70 • written 5 hours ago by
ChumBucket2024
• 0
0
votes
1
reply
62
views
How do I generate a Manhattan plot like this?
data-visualization
manhattan-plot
updated 57 minutes ago by
ATpoint
88k • written 6 hours ago by
jianhua.mert
• 0
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
0
votes
2
replies
159
views
ATAC seq: from peaks to differential analysis ??
MACS2
DESeq2
ATACseq
updated 12 hours ago by
rfran010
★ 1.5k • written 23 hours ago by
Picasa
▴ 680
1
vote
1
reply
102
views
Where to find expected copy number for a gene
genomics
updated 10 hours ago by
GenoMax
151k • written 14 hours ago by
LayneSadler
▴ 90
0
votes
4
replies
1.0k
views
Cut&Run replicates handling
peakcaller
replicates
SEACR
chipseq
updated 14 hours ago by
schowdhury8950
• 0 • written 12 months ago by
g.anande
• 0
0
votes
1
reply
96
views
Unable to extract count matrices from multi-layered Seurat object
seurat
16 hours ago by
bgbs
• 0
13
votes
12
replies
471
views
7 follow
Learning Nextflow
Genomic
Pipeline_analysis
Nextflow
16 hours ago by
AIMAR
▴ 10
3
votes
1
reply
194
views
open target platform SNP to Gene qurey
SNPtoGene
GWAS
SNP
updated 1 day ago by
GenoMax
151k • written 2 days ago by
SeoG
▴ 10
0
votes
1
reply
162
views
usage of ChromHMM and Segway
ChromHMM
Segway
updated 17 hours ago by
Pierre Lindenbaum
166k • written 1 day 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 2 days ago by
fileyfood
▴ 20 • written 8.7 years ago by
Hamtaro
▴ 60
8
votes
4
replies
1.4k
views
Tools for predicting protein function?
protein
updated 2 days ago by
fileyfood
▴ 20 • written 4.1 years ago by
jamie.pike
▴ 90
8
votes
12
replies
2.7k
views
Map genome positions onto protein coordinates?
pdb
protein
variant
updated 2 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 2 days ago by
fileyfood
▴ 20 • written 2.6 years ago by
andre.arrudalima
▴ 80
2
votes
5
replies
1.3k
views
Simple tools for creation of figures of gene and protein structure
gene
protein
updated 2 days ago by
fileyfood
▴ 20 • written 19 months ago by
andre.arrudalima
▴ 80
5
votes
3
replies
1.2k
views
To create amino acid substitution in protein structure
protein
software
updated 2 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 2 days ago by
fileyfood
▴ 20 • written 15.4 years ago by
Giovanni M Dall'Olio
28k
5
votes
2
replies
2.1k
views
Database Of Structurally Derived Protein Features
uniprot
database
updated 2 days ago by
fileyfood
▴ 20 • written 11.2 years ago by
samesense
▴ 50
2
votes
3
replies
1.7k
views
Protein structure and snps
gene
SNP
updated 2 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 2 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 2 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 2 days ago by
fileyfood
▴ 20 • written 9.3 years ago by
sviatoslav.kendall
▴ 980
1
vote
1
reply
206
views
Should I perform integration to correct batch effects?
batch
effect
3 days ago by
han
▴ 10
2
votes
11
replies
585
views
Different comparisons in RNASeq Analysis
DEGs
RNAseq
1 day ago by
SomeOne
▴ 200
0
votes
1
reply
228
views
Querying on non-canonical bacterial IDs
microbes
protein
accession
updated 3 days ago by
Mensur Dlakic
★ 29k • written 3 days ago by
benjamin.kellman
• 0
0
votes
4
replies
350
views
Distribution of assayed SNPs per sample
distribution
PLINK
missingness
1 day ago by
am29
▴ 60
0
votes
0
replies
186
views
News:
Learn Python for Biological Data Analysis – Online Course this September!
NGS
Python
Programming
3 days ago by
Physalia-courses
★ 2.6k
3
votes
0
replies
219
views
Tutorial:
How to calculate partial correlation controlling cancer types
CRISPR
biology
correlation
computational
bioinformatics
4 days ago by
Ming Tommy Tang
★ 4.6k
0
votes
1
reply
250
views
SAIGE-GENE error
R
SAIGE
updated 4 days ago by
GenoMax
151k • written 4 days ago by
smyiz
▴ 30
2
votes
1
reply
1.0k
views
IGV track display problem: interval rectangle from BED file appears above all tracks in white, overlapping each other
IGV
bed
4 days ago by
mcsimenc
▴ 30
2
votes
1
reply
288
views
Y-axis break in Volcano Plot
Volcano_Plot
Enhanced_Volcano
updated 4 days ago by
GenoMax
151k • written 4 days ago by
rajdeepboral00
▴ 70
1
vote
0
replies
228
views
How to rank a gene list using correlation coefficient and p-values for GSEA/clusterProfiler?
ClusterProfiler
GSEA
correlation
rank
genelist
4 days ago by
c-wes
▴ 10
5
votes
4
replies
443
views
Nanopore data analysis
nanopore
updated 4 days ago by
colindaven
7.6k • written 4 days ago by
sarahmanderni
▴ 130
6
votes
2
replies
1.5k
views
What is the difference between norm --multiallelics -any versus --atomize?
bcftools
updated 4 days ago by
ashotmarg2004
▴ 130 • written 21 months ago by
a615ebfb
▴ 50
0
votes
1
reply
264
views
checking the sequences that share origin
sequencing
updated 4 days ago by
GenoMax
151k • written 4 days ago by
QX
▴ 70
0
votes
0
replies
226
views
News:
Assembling Genomes with Oxford Nanopore: A Hands-On Guide to Long-Read Sequencing
Nanopore
GenomeAssembly
longreads
5 days ago by
Physalia-courses
★ 2.6k
0
votes
2
replies
343
views
Bambu on illumina short reads sequencing
Bambu
updated 4 days ago by
Rob
7.1k • written 5 days ago by
Simone
• 0
0
votes
0
replies
230
views
Isoquant Major Exon Elongation
isoquant
nanopore
exon
5 days ago by
aico
• 0
0
votes
0
replies
239
views
bcftools run-roh error
roh
bcftools
updated 5 days ago by
GenoMax
151k • written 5 days ago by
Pratiksha
• 0
0
votes
0
replies
246
views
News:
Workshop: Virtual Single-Cell Transcriptomics, June 24–26
Transcriptomics
workshop
UConn
5 days ago by
zsc25001
▴ 10
1
vote
6
replies
445
views
How can I find KO IDs for ORF sequences from kofam_scan ?
biology
Computational
Bioinformatics
5 days ago by
Nikesh
• 0
0
votes
0
replies
257
views
VEP all genes are skipped due to invalid types
variants
GTF
VEP
annotation
5 days ago by
Titus
▴ 910
4
votes
3
replies
427
views
Isoform analysis after quantification with Salmon/Star
STAR
Salmon
Isoform
analysis
4 days ago by
rajdeepboral00
▴ 70
0
votes
0
replies
241
views
Confidence in CIBERSORT (LM22) Deconvolution Output for Rare Cell Types — Best Practices?
LM22
DECONVOLUTION
CIBERSORT
5 days ago by
Pumla
• 0
1
vote
7
replies
528
views
Significant reads loss after fastp
fastp
loss
reads
updated 4 days ago by
GenoMax
151k • written 5 days ago by
SpliceAndScript
• 0
1
vote
1
reply
313
views
Shinyapps Server Down?
Shinyapps
Posit
updated 5 days ago by
GenoMax
151k • written 5 days ago by
Arup Ghosh
3.3k
0
votes
2
replies
374
views
Data of microarray
Microarray
5 days ago by
Peter
• 0
0
votes
0
replies
282
views
How to run GSVA on scRNA-Seq analysis on multiple clusters and groups to compare per tumor sample?
GSVA
scRNA-Seq
5 days ago by
Minh-Anh
▴ 10
121,384 results • Page
1 of 2428
Recent Votes
Answer: What are the advantages of using the T2T as a reference vs GRCh38 today?
kraken2table, an analogous to kaiju2table
kraken2table, an analogous to kaiju2table
C: Help needed with LOHHLA pipeline
C: Help needed with LOHHLA pipeline
Comment: Where to find expected copy number for a gene
Impact of the number of PCs on the clustering in scRNA seq
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Comment: Best way to install R packages on an HPC?
by
QX
▴ 70
I have no idea if they have some environment manager like `conda`. but I usually make a specific path for R packages for each project, …
Comment: How do I generate a Manhattan plot like this?
by
ATpoint
88k
That could easily be done with ggplot2. Essentially, it comes down to x = chr y = -log10(p) color = locus_type label = th…
Comment: Best way to install R packages on an HPC?
by
ATpoint
88k
The `BiocManager::install` should not take that long, something is wrong, but lack of details stops from investigating this. The writable t…
Comment: Parameters for annotation with maker
by
Jiaxin
• 0
Hi san, Have you got an answer? I would like to put a non-mask genome and a gff file of repetitions as you, will this option work well?
Comment: Status of maker annotation
by
Jiaxin
• 0
Hi Juke, I have the same question as you, have you got an answer?
Answer: Snakemake Module Error: string indices must be integers
by
andean
• 0
I've resolved this by passing the config file via module haplo_call: snakefile: "/home/ac.aleman/git/GATK_haplotype_module/work…
Comment: Snakemake Module Error: string indices must be integers
by
andean
• 0
My guess is that the config file of the parent snakefile is passed as a string to the module rather than a dictionary as usual. How could I…
Comment: Where to find expected copy number for a gene
by
GenoMax
151k
Based on the current gene annotation found in https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_48/gencode.v48.annotation.g…
Answer: ATAC seq: from peaks to differential analysis ??
by
rfran010
★ 1.5k
I also recommend converting the peak to SAF file as QX shows, although I just count fragments centered on cut site. There's little differen…
Comment: CUT&RUN analysis pipeline
by
schowdhury8950
• 0
@rpolicastro Hi, could you please help me understand which type of control is most appropriate for peak calling in CUT&RUN using MACS2? Whi…
Comment: Cut&Run replicates handling
by
schowdhury8950
• 0
Hi there, were you able to find an effective approach for handling replicates in CUT&RUN data? Also, for peak calling, did you use IgG or i…
Answer: Unable to extract count matrices from multi-layered Seurat object
by
bgbs
• 0
Alright, I fixed the issue by joining the counts layers in all_combined. I saved it to a new seurat object. Hopefully this helps someone el…
Comment: Learning Nextflow
by
AIMAR
▴ 10
Thanks for the share I appreciate .
Comment: usage of ChromHMM and Segway
by
Pierre Lindenbaum
166k
cross posted: https://stackoverflow.com/questions/79666471/usage-of-chromhmm-and-segway
Answer: Learning Nextflow
by
Juke34
9.2k
Here the nice ressources I have collected * [Nextflow Training from Fundamentals to Advanced](https://training.nextflow.io/latest/) The o…
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