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1,000 results • Page
2 of 20
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
159
views
Designing single-stable RNA molecules
structure
RNA
4 days ago by
Edna
• 0
0
votes
0
replies
171
views
How to visualize/predict the final transcript from Delly output?
WGS
DELLY
4 days ago by
simplitia
▴ 130
0
votes
1
reply
215
views
Normalize scRNAseq data to housekeeping genes to compare several datasets
RNA-sequencing
housekeeping
Single-cell
normalization
updated 5 days ago by
ATpoint
82k • written 5 days ago by
AaronJaime
• 0
0
votes
0
replies
165
views
Is there a way to increase the automatic label text size in Cytoscape?
Cytoscape
5 days ago by
avocado123
• 0
0
votes
0
replies
152
views
How to calculate correlation coefficient for chipseq?
chipseq
bigwigsummary
correlation
5 days ago by
Emily
▴ 10
1
vote
0
replies
165
views
How to calculate reliable Ka/Ks or dN/dS ratio for genes of interest from VCF file
dnds
kaks
VCF
5 days ago by
rohitsatyam102
▴ 850
0
votes
0
replies
151
views
how to read graph_test output of monocle 3
monocle3
5 days ago by
synat.keam
▴ 100
0
votes
1
reply
483
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
updated 5 days ago by
ginellegrenier
• 0 • written 4 months ago by
Clayton
• 0
0
votes
0
replies
148
views
Why not use iBAQ for calculating differential abundance of proteins?
protein
maxquant
5 days ago by
Aspire
▴ 310
0
votes
3
replies
288
views
Highest variable features in single cell data
single-cell
updated 3 days ago by
bk11
★ 2.4k • written 5 days ago by
Kazo
▴ 10
1
vote
3
replies
350
views
PCA plot
DESeq2
PCAplot
updated 2 days ago by
LauferVA
4.2k • written 5 days ago by
Aaliya
▴ 10
0
votes
0
replies
145
views
Can you give me an example of a small globular protein (PDB) that has disordered alpha-carbons?
protein
pdb
alpha-carbon
5 days ago by
4fzcgueyp5
• 0
0
votes
2
replies
252
views
Annovar using R package
Annovar
gnomAD
R
4 days ago by
DKA
▴ 40
0
votes
5
replies
346
views
Is it possible to get a list of representative genomes from a past RefSeq release?
representative
ncbi
asembly
refseq
updated 5 days ago by
GenoMax
141k • written 6 days ago by
Bertalan_Takacs
▴ 90
0
votes
0
replies
140
views
One error problem occurred caused by data type during using GDCprepare to handle BRCA data
TCGA
GDCprepare
updated 6 days ago by
Ram
43k • written 6 days ago by
glaciya2018
• 0
0
votes
0
replies
306
views
roary not working with pgap output gff files with fasta sequence but works with prokka's gff outputs
pangenome
PGAP
NCBI
roary
Prokka
6 days ago by
pramach1
▴ 40
0
votes
1
reply
161
views
GEMMA GWAS how to specify factor or numerical for covariates
covariate
GEMMA
GWAS
updated 6 days ago by
Sofia
• 0 • written 6 days ago by
mawigoj318
• 0
0
votes
0
replies
142
views
Sequence BLAST in plus/minus and plus/plus
blast
CRISPR
strand
sequencing
6 days ago by
salias
• 0
0
votes
5
replies
345
views
different FeatureCounts output for the same data
fpkm
Counts
Rsubread
rna-seq
updated 3 days ago by
Istvan Albert
100k • written 6 days ago by
sehriban.buyukkilic
▴ 10
0
votes
0
replies
121
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 6 days ago by
Ram
43k • written 6 days ago by
newuser2024
• 0
1
vote
2
replies
231
views
alignment result
RNA-seq
samtools
hisat2
5 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
105
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 6 days ago by
Ram
43k • written 6 days ago by
Jeyong
• 0
0
votes
0
replies
113
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
6 days ago by
Kash
▴ 110
0
votes
1
reply
158
views
How to solve this RoseTTAFold colaboratory error?
modeling
Google
Colaboratory
RoseTTAFold
protein
updated 6 days ago by
Mensur Dlakic
★ 27k • written 6 days ago by
benguyarenbeyaz98
• 0
2
votes
2
replies
280
views
How to calculate identity percentage between proteins contained in a FASTA file?
protein
FASTA
alignment
updated 6 days ago by
Ram
43k • written 6 days ago by
v.berriosfarias
▴ 140
2
votes
9
replies
856
views
TCGA2STAT Error: Firehose connection
FIREHOSE
TCGA
updated 6 days ago by
LauferVA
4.2k • written 6 months ago by
Gnana
• 0
0
votes
11
replies
540
views
How do I use the STARSolo aligner with MGI DNBelab C series HT scRNAseq libraries?
STARSolo
scRNA-seq
STAR
snRNA-seq
MGI
4 days ago by
atowns21
• 0
0
votes
1
reply
167
views
Find subcluster under a cluster, find differential genes in one cluster between 2 samples??
clustering
subclustering
scRNAseq
updated 7 days ago by
bk11
★ 2.4k • written 7 days ago by
alphaflylizard
• 0
0
votes
0
replies
102
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
7 days ago by
ohtang7
▴ 40
0
votes
1
reply
169
views
Plot DNA methylation level of DMR on the basis of certain genes
rrbs
methylkit
updated 7 days ago by
GenoMax
141k • written 7 days ago by
Srinka
▴ 20
0
votes
5
replies
329
views
Should I remove unlocalized scaffols in reference genome before alignment?
qualimap
alignment
minimap2
GRCh38
assembly
6 days ago by
njornet
▴ 20
0
votes
0
replies
96
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 7 days ago by
Ram
43k • written 7 days ago by
SHREYA
• 0
0
votes
0
replies
103
views
Merging replicates from Encode project
CHIP-seq
encode
7 days ago by
Nurken
• 0
1
vote
3
replies
240
views
Filter BAM to keep only alignments at an interval, ignoring reads spliced over
samtools
bam
splicing
7 days ago by
WouterDeCoster
47k
1
vote
3
replies
277
views
some error in building kraken2 database
metagenome
kraken2
6 days ago by
Art1ess
• 0
0
votes
1
reply
156
views
Subset Seurat object from Xenium spatial data
Seurat
Xenium
Spatial
updated 7 days ago by
bk11
★ 2.4k • written 7 days ago by
Susmita Mandal
▴ 110
1
vote
1
reply
178
views
Failed kmer content
kmer
illumina
ngs
updated 7 days ago by
Ram
43k • written 7 days ago by
Kasturi
• 0
0
votes
0
replies
93
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 7 days ago by
Ram
43k • written 7 days ago by
SSSJec
• 0
0
votes
1
reply
150
views
Identification of Transgene insertion sites
Transgene
Whole-Genome-Sequencing
transgene-sites
updated 8 days ago by
Ram
43k • written 8 days ago by
Cameron.walker9900
• 0
0
votes
8
replies
343
views
Error in cnetplot enrichplot package
R
updated 7 days ago by
Ram
43k • written 8 days ago by
Farhad
• 0
0
votes
0
replies
112
views
Pairwise alignment and Ka/Ks computation
Pairwise-Alignment
Genomics
Ka-Ks
updated 8 days ago by
Ram
43k • written 8 days ago by
maxime.policarpo
▴ 200
0
votes
0
replies
96
views
Analysis of the gene family of a genome.
Genome
gene-family
updated 8 days ago by
Ram
43k • written 8 days ago by
sansan_96
▴ 80
0
votes
0
replies
102
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 7 days ago by
Ram
43k • written 8 days ago by
Amélie
• 0
0
votes
0
replies
204
views
Meta analysis of two GWAS summary statistics: one study is case-control and the other is quantitative
GWAS
Meta-analysis
updated 8 days ago by
Ram
43k • written 8 days ago by
Oak
▴ 10
1
vote
3
replies
2.5k
views
Problem to remove subset of patients with plink
plink
PED
updated 7 days ago by
chrchang523
10k • written 6.1 years ago by
Ginevra
▴ 10
1
vote
8
replies
391
views
Downsampling fastq file
downsample
fastq
2 hours ago by
marco.barr
▴ 80
0
votes
1
reply
140
views
tbtool
tbtool
updated 8 days ago by
Ram
43k • written 8 days ago by
Raman
• 0
0
votes
10
replies
448
views
Low mapping rate with Salmon
RNA-seq
Salmon
Quantification
updated 10 hours ago by
i.sudbery
19k • written 8 days ago by
Patadu94
• 0
0
votes
1
reply
133
views
Displaced fragment length distribution in ATAC-seq
ATAC-seq
nucleosome
fragment
updated 8 days ago by
ATpoint
82k • written 8 days ago by
enanoide
• 0
0
votes
0
replies
91
views
Help with finding conferences in immuno-informatics/virology
virology
conferences
immunology
8 days ago by
manaswwm
▴ 510
1,000 results • Page
2 of 20
Recent Votes
Comment: Programmatically retrieving positions of protein active site residues
Comment: Programmatically retrieving positions of protein active site residues
Extracting genomic feature sequences from GTF/GFF files with AGAT
C: Problem with Ensembl version identifiers after running DESeq2
Answer: p-value in CIBERSORT
CTO/founding engineer role at Voyant Bio
Programmatically retrieving positions of protein active site residues
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Comment: What does it mean single base resolution in sequencing?
by
LauferVA
4.2k
this is very true and increasingly true as time goes forward. thanks for supplementing this post with your own :-)
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
jeffrey.maurer.informatics
• 0
Thank you, but I've already checked out that site to see if I was missing anything and I don't see any answers to my questions there.
Answer: p-value in CIBERSORT
by
Aspire
▴ 310
You have not explicitly specified the number of permutations (which are used to calculate the p-value). The default value of the permutatio…
Comment: Telescope issue
by
GenoMax
141k
> CIGAR and query sequence are of different length [W::sam_read1] Parse error at line 9954941 Problem appears to be at that line. Can you …
Comment: KEGG Pathways
by
Ram
43k
Give us as much detail as you can. What error does it give you?
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
by
GenoMax
141k
SRA Run Selector shows a better view of the metadata: https://www.ncbi.nlm.nih.gov/Traces/study/?acc=PRJNA761679&o=acc_s%3Aa
Comment: Adjust pvalue in R with different approach give me all different outcome
by
Aspire
▴ 310
- p.adjust() is supposed to receive a **numeric vector of p-values**, not a matrix. - It makes no sense to "adjust" just one p-value, as…
Comment: Downsampling fastq file
by
marco.barr
▴ 80
I understood where the problem lies. I discussed with my wet lab colleagues (this is part of a bioinformatician's job...) and by showing th…
Comment: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This question fits in nicely with the [SIB Swiss Institute of Bioinformatics course on Enzyme information in UniProt][1] [1]: https://w…
Answer: Programmatically retrieving positions of protein active site residues
by
me
▴ 760
This can be done via SPARQL at the UniProt.org sparql endpoint PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#> PREFIX fald…
Comment: KEGG Pathways
by
Sudip
• 0
No it does not. Do you know of a way that can help me achieve what I want?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
GenoMax
141k
UniRef file is 43G compressed so probably will become ~60G when uncompressed. You would likely be looking at at least that much +10-20% GB …
Comment: RNAseq one control two conditions, shared and exclusive genes
by
matteo.levorato
• 0
thank you for your comment, but yes running DESeq2 is the starting point. dds <- DESeqDataSetFromMatrix(countData=RawCounts, …
Comment: Need help for downloading arabdopsis thaliana reference genome fasta file and gt
by
Ram
43k
Please stop pasting a sentence in the `tags` field. That field is for subject matter keywords. I've fixed your posts this time, please be m…
Comment: KEGG Pathways
by
Ram
43k
> is the below code correct Does it give you what you need?
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