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1,000 results • Page
1 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
11
views
Designing single-stable RNA molecules
structure
RNA
20 minutes ago by
Edna
• 0
0
votes
0
replies
17
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
16 minutes ago by
simplitia
▴ 130
0
votes
1
reply
36
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
AaronJaime
• 0
0
votes
0
replies
40
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
4 hours ago by
avocado123
• 0
0
votes
0
replies
37
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
4 hours ago by
Emily
▴ 10
1
vote
0
replies
46
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
4 hours ago by
rohitsatyam102
▴ 850
0
votes
0
replies
39
views
how to read graph_test output of monocle 3
monocle3
5 hours ago by
synat.keam
▴ 100
0
votes
1
reply
373
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 6 hours ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
57
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
12 hours ago by
Aspire
▴ 300
0
votes
2
replies
137
views
Highest variable features in single cell data
single-cell
updated 1 hour ago by
Ram
43k • written 14 hours ago by
Kazo
• 0
0
votes
1
reply
126
views
PCA plot
DESeq2
PCAplot
updated 6 hours ago by
jkim
▴ 170 • written 18 hours ago by
Aaliya
▴ 10
0
votes
0
replies
83
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
20 hours ago by
4fzcgueyp5
• 0
0
votes
2
replies
150
views
Annovar using R package
Annovar
gnomAD
R
49 minutes ago by
DKA
▴ 40
0
votes
5
replies
261
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 8 hours ago by
GenoMax
141k • written 1 day ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
110
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 1 day ago by
Ram
43k • written 1 day ago by
glaciya2018
• 0
0
votes
0
replies
204
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
1 day ago by
pramach1
▴ 40
0
votes
1
reply
127
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 1 day ago by
Sofia
• 0 • written 1 day ago by
mawigoj318
• 0
0
votes
0
replies
114
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
1 day ago by
salias
• 0
0
votes
4
replies
236
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
12 hours ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
100
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 1 day ago by
Ram
43k • written 1 day ago by
newuser2024
• 0
1
vote
2
replies
181
views
alignment result
RNA-seq
samtools
hisat2
15 hours ago by
ahmad.sajad4541
• 0
0
votes
0
replies
91
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 1 day ago by
Ram
43k • written 1 day ago by
Jeyong
• 0
0
votes
0
replies
103
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
1 day ago by
Kash
▴ 110
0
votes
1
reply
138
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
227
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 1 day ago by
Ram
43k • written 2 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
814
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
399
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
147
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
alphaflylizard
• 0
0
votes
0
replies
91
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
2 days ago by
ohtang7
▴ 40
0
votes
1
reply
148
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 2 days ago by
GenoMax
141k • written 2 days ago by
Srinka
▴ 20
0
votes
5
replies
281
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
1 day ago by
njornet
▴ 20
0
votes
0
replies
84
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 2 days ago by
Ram
43k • written 2 days ago by
SHREYA
• 0
0
votes
0
replies
93
views
Merging replicates from Encode project
CHIP-seq
encode
2 days ago by
Nurken
• 0
1
vote
3
replies
199
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
2 days ago by
WouterDeCoster
47k
1
vote
3
replies
237
views
some error in building kraken2 database
metagenome
kraken2
1 day ago by
Art1ess
• 0
0
votes
1
reply
125
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
160
views
Failed kmer content
kmer
illumina
ngs
updated 2 days ago by
Ram
43k • written 2 days ago by
Kasturi
• 0
0
votes
0
replies
81
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 2 days ago by
Ram
43k • written 2 days ago by
SSSJec
• 0
0
votes
1
reply
140
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 3 days ago by
Ram
43k • written 3 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
295
views
Error in cnetplot enrichplot package
R
updated 3 days ago by
Ram
43k • written 3 days ago by
Farhad
• 0
0
votes
0
replies
105
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 3 days ago by
Ram
43k • written 3 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
90
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 3 days ago by
Ram
43k • written 3 days ago by
sansan_96
▴ 80
0
votes
0
replies
92
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 2 days ago by
Ram
43k • written 3 days ago by
Amélie
• 0
0
votes
0
replies
178
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 3 days ago by
Ram
43k • written 3 days ago by
Oak
▴ 10
1
vote
3
replies
2.4k
views
Problem to remove subset of patients with plink
plink
PED
updated 3 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
5
replies
253
views
Downsampling fastq file
downsample
fastq
updated 3 days ago by
Ram
43k • written 3 days ago by
marco.barr
▴ 80
0
votes
1
reply
124
views
tbtool
tbtool
updated 3 days ago by
Ram
43k • written 3 days ago by
Raman
• 0
0
votes
2
replies
188
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 3 days ago by
i.sudbery
19k • written 3 days ago by
Patadu94
• 0
0
votes
1
reply
119
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 3 days ago by
ATpoint
82k • written 3 days ago by
enanoide
• 0
0
votes
0
replies
82
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
3 days ago by
manaswwm
▴ 490
1,000 results • Page
1 of 20
Recent Votes
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
Detecting somatic variants in non-tumor tissue without normals
Answer: Sequence read length shorter than flow cell specification
Answer: Sequence read length shorter than flow cell specification
Comment: Why gatk VariantAnnotator required bam and coverage files
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Visualization of ChIP-seq data using Heatmaps (Updated: 06/10/16)
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82k
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▴ 30
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Recent Replies
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Ram
43k
Thank you, the `csvtk spread` is super useful. I usually import into R using `lapply` then `Reduce` using `merge` but this might be easier.
Comment: Annovar using R package
by
DKA
▴ 40
Thank you for your guidance. The thing is that I am unfamiliar with using such environments, unfortunately.
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
ATpoint
82k
Open a new question, with details.
Comment: Normalize scRNAseq data to housekeeping genes to compare several datasets
by
ATpoint
82k
I recommend https://bioconductor.org/books/3.18/OSCA.basic/normalization.html as well as the "advanced" section in this book.
Comment: Why gatk VariantAnnotator required bam and coverage files
by
QX
• 0
thank you!
Comment: Treatment VS Control in Single Cell RNAseq analysis
by
kilcdincer
▴ 10
Hello, I have more or less same experimental setting and was wondering how you proceeded with your analysis? Can I reach its GitHub reposit…
Comment: BLAST using both nucleotides and taxonomic local databases
by
GenoMax
141k
> I ask this as some BLAST command fields as scinames or sblastnames do not give any output with a classic nt BLAST If that information is…
Answer: BLAST using both nucleotides and taxonomic local databases
by
5heikki
11k
This has been discussed [many times][1] [1]: https://www.biostars.org/p/76551/
Answer: why renaming Idents in Seurat object doesn't work?
by
Bioinfotec
▴ 10
I think when you give indent to seuObj : Idents(seuObj) <- 'RNA_snn_res.0.1' You may wrongly assign other value to it such as …
Answer: ScRNAseq-How to correctly choose cell type marker genes
by
Bioinfotec
▴ 10
In fact, there is no gold standard for cell type annotation. To achieve correct cell type classification, you can combine the two methos. F…
Answer: ScRNA data question
by
Bioinfotec
▴ 10
In violin plot, a dot represents a cell. Actually, the straight lines you see in your infected image just means these cells have the same e…
Comment: Sequence read length shorter than flow cell specification
by
GenoMax
141k
> the have sent data with different sequencing read lengths: 55bp pair ended and 80bp single ended If they sent data that is not what you…
Comment: How to know synonymous and non-synonymous SNPs from transcriptome sequencing
by
rohitsatyam102
▴ 850
I have some off-the-chart dN/dS values for few genes (>20) when using your script on VCF obtained from a 20K plasmodium genomes (pf7K). | …
Answer: Sequence read length shorter than flow cell specification
by
ATpoint
82k
It is the amount of reagent in the kit that determines read length. Sometimes index cycle reagents are allocated to R1/R2 or they used anot…
Comment: Why gatk VariantAnnotator required bam and coverage files
by
Pierre Lindenbaum
161k
you don't need the bam file https://gatk.broadinstitute.org/hc/en-us/articles/13832654601755-VariantAnnotator : VariantAnnotator …
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