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106 results • Page
1 of 3
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Votes
Replies
0
votes
1
reply
19
views
Highest variable features in single cell data
cell
single
updated 11 minutes ago by
ATpoint
82k • written 43 minutes ago by
Kazo
• 0
0
votes
0
replies
38
views
PCA plot
DESeq2
PCAplot
4 hours ago by
Aaliya
▴ 10
0
votes
0
replies
55
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
6 hours ago by
4fzcgueyp5
• 0
0
votes
1
reply
107
views
Annovar using R package
Annovar
gnomAD
R
updated 9 hours ago by
Pierre Lindenbaum
161k • written 11 hours ago by
DKA
▴ 40
0
votes
0
replies
64
views
Finding orthologs between genome error
OMA
OMAbrowser
14 hours ago by
hemantcnaik
• 0
0
votes
0
replies
77
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 12 hours ago by
Ram
43k • written 17 hours ago by
glaciya2018
• 0
0
votes
0
replies
128
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
17 hours ago by
pramach1
▴ 40
0
votes
1
reply
103
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 16 hours ago by
Sofia
• 0 • written 20 hours ago by
mawigoj318
• 0
0
votes
0
replies
87
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
21 hours ago by
salias
• 0
0
votes
2
replies
150
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 12 hours ago by
Ram
43k • written 22 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
78
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 12 hours ago by
Ram
43k • written 22 hours ago by
newuser2024
• 0
1
vote
2
replies
128
views
alignment result
RNA-seq
samtools
hisat2
1 hour ago by
ahmad.sajad4541
• 0
0
votes
0
replies
70
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 12 hours ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
0
replies
81
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
1
reply
120
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 1 day ago by
Mensur Dlakic
★ 27k • written 1 day ago by
benguyarenbeyaz98
• 0
0
votes
2
replies
204
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 12 hours ago by
Ram
43k • written 1 day ago by
v.berriosfarias
▴ 140
2
votes
9
replies
797
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
363
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
1 day ago by
atowns21
• 0
0
votes
1
reply
133
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
87
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
1 day ago by
ohtang7
▴ 40
0
votes
1
reply
143
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
273
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
20 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
190
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
228
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
157
views
Failed kmer content
kmer
illumina
ngs
updated 1 day ago by
Ram
43k • written 2 days ago by
Kasturi
• 0
0
votes
0
replies
80
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 2 days 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
280
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
103
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
86
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
152
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
243
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
177
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
71
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
239
views
interpretartion of a vcf file
calling
genotype
ONT
variant
diploid
23 hours ago by
samuelkalandarov2002
▴ 10
0
votes
0
replies
77
views
Annotating single cell data automatically
cell
annotation
single
2 days ago by
Gerard
• 0
0
votes
1
reply
140
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
69
views
Imputation advice
imputation
2 days ago by
kl
▴ 10
0
votes
0
replies
84
views
Trimming best practices for SNP calling
trimming
SNP
trimmomatic
2 days ago by
Enrique
• 0
0
votes
0
replies
70
views
Correct way of reducing predictive model complexity
lasso
glmnet
predictvemodeling
regression
3 days ago by
sativus
▴ 20
0
votes
0
replies
76
views
Difficulties getting **the adjacency file** necessary for **aracne2regulon** function.
VIPER
MARINA
ARACNe
3 days ago by
Biostars2200
• 0
106 results • Page
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Recent Votes
Comment: alignment result
Comment: clustalo - align milions of short seq, memory issue
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)
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Recent Replies
Answer: Figures are disappeared from html report of SnpEff
by
Pierre Lindenbaum
161k
the remote website providing the javascript or/and the images is down or you're now behind a proxy. Check the firefox console: https://fire…
Comment: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
ah ! and your code doesn't work because clinvar ID is not a rs-ID.
Answer: Fetch table from clinvar database according to a list of rsid
by
Pierre Lindenbaum
161k
$ cat input.rs rs11203366 rs11203367 rs874881 rs776453694 rs80324279 rs324420 rs112766203 wget -…
Comment: Highest variable features in single cell data
by
ATpoint
82k
> and these cells are not even in a single cluster. What does this mean? If you run clustering on all cells then every cell is assigned t…
Comment: Is it possible to get a list of representative genomes from a past RefSeq releas
by
Bertalan_Takacs
▴ 90
Yes, I can tell that, but as far as I see it doesn't contain any other information about the genomes, such as if they were representative i…
Answer: Hide positions in alignment with 99% "–" characters to ignore single sequence in
by
b.contreras.moreira
▴ 170
You can try <https://github.com/inab/trimal>
Comment: To get p-values for the TPM
by
VITALA
• 0
yes i want what rsem does and i did try with prior-enhanced option/pRSEM, but i think pRSEM is for chipseq data
Comment: alignment result
by
ahmad.sajad4541
• 0
Thank you so much. Should i proceed for annotation step?
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
The code you already posted in the bioconductor board had simulated data, and the PCA image is the same.
Answer: Network Alignment
by
Scooter
▴ 280
Unfortunately, it's not working for me either, and the web site doesn't exist anymore. You might try reaching out to the authors, but I kn…
Answer: How could I generate a gi_taxid_nucl.dmp file similar to the one previously host
by
ZhangYuanfeng
• 0
JUST GIVE THE ANSWER! Here is the solution: ```bash aria2c -c -s 4 -j 4 \ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/accession2taxid/pd…
Comment: PCA plot (Suggestions Needed)
by
Aaliya
▴ 10
I have actually used DESeq2 data.
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
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