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109 results • Page
1 of 3
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Views
Votes
Replies
0
votes
0
replies
38
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
1 hour ago by
4fzcgueyp5
• 0
0
votes
1
reply
80
views
Annovar using R package
Annovar
gnomAD
R
updated 4 hours ago by
Pierre Lindenbaum
161k • written 6 hours ago by
DKA
▴ 40
0
votes
0
replies
51
views
Finding orthologs between genome error
OMA
OMAbrowser
9 hours ago by
hemantcnaik
• 0
0
votes
0
replies
68
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 7 hours ago by
Ram
43k • written 12 hours ago by
glaciya2018
• 0
0
votes
0
replies
98
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
12 hours ago by
pramach1
▴ 40
0
votes
1
reply
95
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 11 hours ago by
Sofia
• 0 • written 15 hours ago by
mawigoj318
• 0
0
votes
0
replies
77
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
17 hours ago by
salias
• 0
0
votes
2
replies
140
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 7 hours ago by
Ram
43k • written 17 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
69
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 7 hours ago by
Ram
43k • written 17 hours ago by
newuser2024
• 0
0
votes
0
replies
60
views
Network Alignment
plugin
Cytoscape
CytoMCS
18 hours ago by
Akash D
▴ 40
0
votes
1
reply
107
views
alignment result
RNA-seq
samtools
hisat2
updated 7 hours ago by
Ram
43k • written 18 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
60
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 7 hours ago by
Ram
43k • written 20 hours ago by
Jeyong
• 0
0
votes
0
replies
75
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
1
reply
113
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 22 hours ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
195
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 7 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
9
replies
787
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 1 day ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
10
replies
354
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
23 hours ago by
atowns21
• 0
0
votes
1
reply
126
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
alphaflylizard
• 0
0
votes
0
replies
82
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
0
votes
1
reply
137
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Srinka
▴ 20
0
votes
5
replies
263
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
15 hours ago by
njornet
▴ 20
0
votes
0
replies
81
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 1 day ago by
Ram
43k • written 1 day ago by
SHREYA
• 0
0
votes
0
replies
90
views
Merging replicates from Encode project
CHIP-seq
encode
1 day ago by
Nurken
• 0
1
vote
3
replies
189
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
1 day ago by
WouterDeCoster
47k
1
vote
3
replies
225
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
0
votes
1
reply
119
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 1 day ago by
bk11
★ 2.3k • written 1 day ago by
Susmita Mandal
▴ 110
1
vote
1
reply
152
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 1 day ago by
Kasturi
• 0
0
votes
0
replies
78
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 1 day ago by
Ram
43k • written 1 day ago by
SSSJec
• 0
0
votes
1
reply
132
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 2 days ago by
Ram
43k • written 2 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
277
views
Error in cnetplot enrichplot package
R
updated 2 days ago by
Ram
43k • written 2 days ago by
Farhad
• 0
0
votes
0
replies
102
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 2 days ago by
Ram
43k • written 2 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
85
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 2 days ago by
Ram
43k • written 2 days ago by
sansan_96
▴ 80
0
votes
0
replies
90
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 1 day ago by
Ram
43k • written 2 days ago by
Amélie
• 0
0
votes
0
replies
144
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 2 days ago by
Ram
43k • written 2 days ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 2 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
239
views
Downsampling fastq file
downsample
fastq
updated 2 days ago by
Ram
43k • written 2 days ago by
marco.barr
▴ 80
0
votes
1
reply
121
views
tbtool
tbtool
updated 2 days ago by
Ram
43k • written 2 days ago by
Raman
• 0
0
votes
2
replies
176
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 2 days ago by
i.sudbery
19k • written 2 days ago by
Patadu94
• 0
0
votes
1
reply
114
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 2 days ago by
ATpoint
82k • written 2 days ago by
enanoide
• 0
0
votes
0
replies
80
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
2 days ago by
manaswwm
▴ 490
0
votes
0
replies
70
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
1 day ago by
alifafiq1
• 0
0
votes
0
replies
78
views
How to get somatic variation based on RNA-seq data?
RNA-seq
variation
somatic
2 days ago by
feather-W
• 0
2
votes
4
replies
236
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
18 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
75
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
1
reply
139
views
RNA-seq bacteria contamination
RNA-seq
updated 2 days ago by
GenoMax
141k • written 2 days ago by
sh
• 0
0
votes
0
replies
68
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
0
votes
0
replies
83
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
0
votes
0
replies
69
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
2 days ago by
sativus
▴ 20
0
votes
0
replies
76
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
2 days ago by
Biostars2200
• 0
0
votes
0
replies
120
views
CIRIquant: ValueError: file has no sequences defined (mode='rb') - is it SAM/BAM format? Consider opening with check_sq=False
Ciriquant
updated 2 days ago by
Carlo Yague
8.7k • written 2 days ago by
Atul K.
• 0
109 results • Page
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Recent Votes
Answer: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Comment: Why cd-hit-est not work when sequence identity threshold<0.95?
by
Dateline
• 0
So, why? I have 18GB of data, and when -c=0.95, the run ends in about two days, while when -c=0.9, it has been three days and only a little…
Answer: Heatmap and rna-seq
by
Kevin Blighe
87k
Hi, you can take the list of GSEA pathways and then use these via GSVA (https://github.com/rcastelo/GSVA) to create a heatmap. You hav…
Comment: Clustering of DAVID gene enrichment results from gene expression studies
by
Kevin Blighe
87k
You will have to elaborate on what is the error
Comment: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
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