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1,000 results • Page
5 of 20
Sort: Rank
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Views
Votes
Replies
2
votes
2
replies
244
views
PDB related issue
rcsb
pdb
updated 19 days ago by
noodle
▴ 580 • written 19 days ago by
Nafi
• 0
0
votes
9
replies
2.6k
views
6 follow
Cannot process all the reads in a fast5 file?
metagenome
base-calling
fastq
nanopore
updated 19 days ago by
Ram
43k • written 9 months ago by
Gio
• 0
1
vote
2
replies
280
views
Downloading full alignments from Pfam
pfam
13 days ago by
bef1
• 0
0
votes
0
replies
140
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 19 days ago by
dariober
14k • written 20 days ago by
rene.j.erhardt
▴ 20
1
vote
3
replies
379
views
How to assign cell types after integration in scRNA
scRNA-seq
updated 19 days ago by
ATpoint
82k • written 20 days ago by
Francesco
▴ 10
0
votes
0
replies
157
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
20 days ago by
tnminh89
▴ 10
0
votes
0
replies
159
views
Filter low express genes in microarray data
microarray
20 days ago by
Chris
▴ 280
0
votes
0
replies
587
views
Correlation between cell type prediction scores and individual gene expression in spatial transcriptomic datasets
single-cell
Spatial-Transcriptomics
21 days ago by
biocellbio
• 0
0
votes
0
replies
226
views
Phasing VCF Files and Analyzing Reads with Multiple Variants
haplotypes
vcf
phasing
22 days ago by
HarperReed
• 0
1
vote
0
replies
175
views
Simulation of label-free bottom-up proteomics expression dataset
label-free
bottom-up
lc-ms
proteomics
22 days ago by
KABILAN
▴ 70
0
votes
0
replies
191
views
Running Phylogenetic Analysis With NCBI Genome
population-genetics
phylogenetic
updated 21 days ago by
Ram
43k • written 22 days ago by
SineWave
• 0
0
votes
0
replies
192
views
RNA-seq: full length gene
RNA-seq
updated 21 days ago by
Ram
43k • written 22 days ago by
Nargis
• 0
0
votes
0
replies
173
views
Haplotype Phased Assembly Contigs to Chromosome Annotations
Assembly
phased
Haplotype
Annotation
22 days ago by
turcoa1
• 0
0
votes
0
replies
185
views
Designing single-stable RNA molecules
structure
RNA
22 days ago by
Edna
• 0
0
votes
0
replies
198
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
22 days ago by
simplitia
▴ 130
1
vote
1
reply
269
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 22 days ago by
ATpoint
82k • written 22 days ago by
AaronJaime
• 0
0
votes
0
replies
183
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
deeptools
correlation
4 days ago by
Emily
▴ 20
1
vote
0
replies
195
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
22 days ago by
rohitsatyam102
▴ 860
0
votes
0
replies
174
views
how to read graph_test output of monocle 3
monocle3
22 days ago by
synat.keam
▴ 100
0
votes
1
reply
537
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 23 days ago by
ginellegrenier
• 0 • written 5 months ago by
Clayton
• 0
0
votes
0
replies
179
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
23 days ago by
Aspire
▴ 330
0
votes
4
replies
422
views
Highest variable features in single cell data
single-cell
11 days ago by
carolofharvest
▴ 40
1
vote
3
replies
451
views
PCA plot
DESeq2
PCAplot
updated 19 days ago by
LauferVA
4.2k • written 23 days ago by
Aaliya
▴ 10
0
votes
0
replies
174
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
23 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
314
views
Annovar using R package
Annovar
gnomAD
R
22 days ago by
DKA
▴ 40
0
votes
5
replies
443
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 23 days ago by
GenoMax
142k • written 24 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
168
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 23 days ago by
Ram
43k • written 24 days ago by
glaciya2018
• 0
0
votes
0
replies
330
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
24 days ago by
pramach1
▴ 40
0
votes
1
reply
210
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 24 days ago by
Sofia
• 0 • written 24 days ago by
mawigoj318
• 0
0
votes
0
replies
169
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
24 days ago by
salias
• 0
0
votes
5
replies
467
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 21 days ago by
Istvan Albert
100k • written 24 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
146
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 23 days ago by
Ram
43k • written 24 days ago by
newuser2024
• 0
1
vote
2
replies
284
views
alignment result
RNA-seq
samtools
hisat2
23 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
141
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
24 days ago by
Kash
▴ 110
0
votes
1
reply
191
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 24 days ago by
Mensur Dlakic
★ 27k • written 24 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
336
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 23 days ago by
Ram
43k • written 24 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
942
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 24 days ago by
LauferVA
4.2k • written 7 months ago by
Gnana
• 0
0
votes
11
replies
716
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
22 days ago by
atowns21
• 0
0
votes
1
reply
213
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 24 days ago by
bk11
★ 2.5k • written 24 days ago by
alphaflylizard
• 0
0
votes
0
replies
120
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
25 days ago by
ohtang7
▴ 40
0
votes
1
reply
209
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 25 days ago by
GenoMax
142k • written 25 days ago by
Srinka
▴ 20
0
votes
5
replies
429
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
24 days ago by
njornet
▴ 20
0
votes
0
replies
127
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 25 days ago by
Ram
43k • written 25 days ago by
SHREYA
• 0
0
votes
0
replies
130
views
Merging replicates from Encode project
CHIP-seq
encode
25 days ago by
Nurken
• 0
1
vote
3
replies
304
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
25 days ago by
WouterDeCoster
47k
1
vote
3
replies
339
views
some error in building kraken2 database
metagenome
kraken2
24 days ago by
Art1ess
• 0
0
votes
1
reply
216
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 25 days ago by
bk11
★ 2.5k • written 25 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
216
views
Failed kmer content
kmer
illumina
ngs
updated 25 days ago by
Ram
43k • written 25 days ago by
Kasturi
• 0
0
votes
0
replies
115
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 25 days ago by
Ram
43k • written 25 days ago by
SSSJec
• 0
0
votes
1
reply
177
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 25 days ago by
Ram
43k • written 25 days ago by
Cameron.walker9900
• 0
1,000 results • Page
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constructing pangenome through psvcp
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Differential Expression with limma: Contrast and Design Matrix, combinatorial approach valid?
Answer: RNAseq coverage vs depth for transcript isoform expression?
Answer: ChatGPT optimized for bioinformatics questions
Comment: ChatGPT optimized for bioinformatics questions
C: How can I perform Differential expression analysis with just one control and one
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mohammadhassanj
▴ 260
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Comment: constructing pangenome through psvcp
by
analyst
▴ 50
Fixed the issue by updating nucmer version.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
GenoMax
142k
Can you create a small test database (`makeblastdb`) from your query file and try to run the search against the same file and see if that w…
Comment: calculating genomic coverage/ base overlap in R
by
1769mkc
★ 1.2k
you can `dput(head(df)` for the both the data frame so that other can test for possible solutions
Comment: Broad and Narrow peaks
by
ATpoint
82k
What is your question? It's unclear.
Comment: Help with Biopython for Beginner
by
Joe
21k
One question before offering more solutions: are you trying to learn Python with this as an example problem, or are you trying to find the …
Answer: RNAseq coverage vs depth for transcript isoform expression?
by
Gordon Smyth
★ 7.2k
See the exploration of isoform precision vs read length and sequencing depth in our paper: https://doi.org/10.1093/nar/gkad1167. Table 1 o…
Comment: How to handle duplicated genes in TCGA data?
by
txema.heredia
▴ 130
Why does the tool require gene symbols and not ensembl ids? Is it retrieving information from somewhere else? If so, your best bet is to fi…
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Thank you so much for your response . Really appreciate it. I will try the way you mentioned and will get back if I have any query
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i have the same error, i used high performance computer, here is my code to set memory. srun --nodes=1 --ntasks=1 --cpus-per-task=24 -…
Comment: Overlapping Ranges within Granges object
by
Alex Reynolds
35k
Yes, `bedmap` will perform operations on one or two BED files.
Comment: B allele frequency (BAF)
by
aidangcruickshank
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Apologies for resurrecting this post, but any idea what that functions "regions" paramater takes? Would it be a GRanges object? The documen…
Comment: How to handle duplicated genes in TCGA data?
by
Ngrin
• 0
Thanks @txema.heredia.The tool I am going to use only accepts gene symbols. This is the reason. So I cannot use ENS IDs.
Answer: Design for complex RNA-Seq experiment using Deseq2
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swbarnes2
14k
This is a rather small experiment, I don't know that you can establish a meaningful baseline for each patient with a single pre sample, and…
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4.2k
@bk11 i changed this comment to an answer. if you disagree please let me know. thanks for sharing your knowledge. VAL
Comment: ComplexHeatmap - How to change fontsize of rowAnnotation
by
hannes.bongartz
• 0
Thanks for the input. Unfortunately, that didn't help either. I appreciate any other tips. Thank you
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