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Limit : this week
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82 results • Page
2 of 2
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Views
Votes
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0
votes
1
reply
133
views
Downloading full alignments from Pfam
pfam
updated 1 day ago by
GenoMax
141k • written 1 day ago by
bef1
• 0
0
votes
0
replies
128
views
Filter low express genes in microarray data
microarray
2 days ago by
Chris
▴ 260
0
votes
3
replies
123
views
Software to separate reads from different individuals
software
development
nanopore
updated 3 hours ago by
GenoMax
141k • written 7 hours ago by
njornet
▴ 20
0
votes
0
replies
122
views
STAR total splices (in Log.final) vs collapsed splice junctions (in SJ.out.tab)
STAR
2 days ago by
tnminh89
▴ 10
0
votes
0
replies
120
views
Alternative splicing analysis using SUPPA tool - how to normalise counts?
rna-seq
single-cell
suppa
alternative-splicing
updated 5 days ago by
Ram
43k • written 5 days ago by
newuser2024
• 0
0
votes
2
replies
113
views
What should I consider as FASTA for dataset?
PDB
FASTA
1 hour ago by
Nafi
• 0
0
votes
0
replies
111
views
AttributeError: module 'scvelo' has no attribute 'pp
loomfile
scvelo
scipy
annData
numpy
5 days ago by
Kash
▴ 110
0
votes
0
replies
103
views
Is result interpretation of the modelHomotypic function of the DoubletFinder correct?
doublet
DoubletFinder
Seurat
modelHomotypic
updated 5 days ago by
Ram
43k • written 5 days ago by
Jeyong
• 0
0
votes
0
replies
102
views
Merging replicates from Encode project
CHIP-seq
encode
6 days ago by
Nurken
• 0
0
votes
2
replies
99
views
Longitudinal analysis of subpopulations: which approach is better?
differential-expression
DEG
model
11 hours ago by
Lluís R.
★ 1.2k
0
votes
0
replies
100
views
The concept of co-occurrence network structure
co-occurence
microbiome
network
6 days ago by
ohtang7
▴ 40
0
votes
2
replies
100
views
How to update R on ubuntu
installation
update
R
apt-get
7 hours ago by
Bosberg
▴ 50
0
votes
0
replies
100
views
File with NCBI summary or Uniprot description
annotation
visualisation
NCBI
Uniprot
RNA
updated 6 days ago by
Ram
43k • written 7 days ago by
Amélie
• 0
0
votes
0
replies
96
views
adjusting for confounders in LMER in R
confounders
LMER
R
updated 6 hours ago by
dariober
14k • written 1 day ago by
rene.j.erhardt
▴ 20
0
votes
0
replies
95
views
Software to calculate RSCU, ENC other than codonw
rscu
codonw
updated 6 days ago by
Ram
43k • written 6 days ago by
SHREYA
• 0
0
votes
1
reply
91
views
Can I merge Hi-C fastq files from different lanes?
GenomeAssembly
BWA-MEM2
Hi-C
updated 10 hours ago by
GenoMax
141k • written 17 hours ago by
Winter
• 0
0
votes
0
replies
88
views
How do I select a GC file (gc.wig)? (How to determine the inputdata of HMMcopy)
HMMcopy
Copy-number-analysis
R
updated 6 days ago by
Ram
43k • written 6 days ago by
SSSJec
• 0
0
votes
2
replies
84
views
Genbank File Format
gbkformat
updated 5 hours ago by
Mensur Dlakic
★ 27k • written 7 hours ago by
alenew.am
• 0
0
votes
0
replies
81
views
Filtering most similarly expressed gene (contrary to differential expression gene) with NOISeq?
NOIseq
6 days ago by
alifafiq1
• 0
0
votes
0
replies
77
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
7 hours ago by
SSSJec
• 0
0
votes
0
replies
63
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
14 hours ago by
atharvakarkare14
▴ 10
0
votes
0
replies
61
views
vg call vs vg surject
vg
variation
graphs
updated 10 hours ago by
GenoMax
141k • written 17 hours ago by
aliraza3119
• 0
0
votes
0
replies
58
views
LEfSe
LEfSe
10 hours ago by
benkosta
• 0
0
votes
0
replies
56
views
Differential accessibility using DiffBinf
diffbind
16 hours ago by
Shloka
• 0
0
votes
1
reply
50
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
kim
• 0
0
votes
0
replies
47
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
8 hours ago by
Sara
▴ 30
0
votes
0
replies
46
views
Synteny analysis
bacterial
synteny
genome
updated 6 hours ago by
GenoMax
141k • written 6 hours ago by
Namil
• 0
0
votes
0
replies
41
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
8 hours ago by
David
• 0
0
votes
0
replies
37
views
Using limma in methylation EM-seq?
EM-seq
methylation
6 hours ago by
Lluís R.
★ 1.2k
0
votes
1
reply
31
views
Differential Accessibility
DiffBind
updated 56 minutes ago by
Ram
43k • written 1 hour ago by
Shloka
• 0
0
votes
0
replies
4
views
Perfom a Gene Ontology Analysis from GO terms file
GO
RNASeq
just now by
Hamtaro
▴ 50
0
votes
0
replies
5
views
Polishing genome assembly
polishing
Nanopore
PacBio
7 minutes ago by
Lissa Cruz Saavedra
• 0
82 results • Page
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Recent Votes
Answer: Extract protein sequence
Answer: Extract protein sequence
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Answer: Source other conda environments in a nextflow pipeline when nextflow itself is i
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
Comment: How to calculate identity percentage between proteins contained in a FASTA file?
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Recent Replies
Answer: Post-imputation plot
by
LChart
3.9k
The anti-diagonal band does suggest some fraction of genotypes are strand-flipped - probably G/C or A/T variants.
Comment: Differential Accessibility
by
Ram
43k
Please do not paste screenshots of plain text content, it is counterproductive. You can copy paste the content directly here (using the cod…
Comment: Extract protein sequence
by
anna
▴ 20
Thank you! I need this for eukaryotic organism and known protein sequences, but I guess seqkit would work well!
Comment: Landmark gene selection in L1000.
by
GenoMax
141k
Paper referred to in question: https://pubmed.ncbi.nlm.nih.gov/29195078/ > so I want to understand how you reduced the 12063 genes to 978…
Comment: What should I consider as FASTA for dataset?
by
Nafi
• 0
Protein attribute prediction
Comment: Batch effects : ComBat or removebatcheffects (limma package) ?
by
cwwong13
▴ 40
@kevin May I know whether your comments and edits were mainly based on the fact that "Previously, [crazy] people had been using the origina…
Comment: Programmatically retrieving positions of protein active site residues
by
Wayne
★ 2.0k
Wow, I was shocked at this AI answer that looks to be a good start for using UniProt. Sharing it in case it is useful. (It will work in ses…
Comment: NGS forensics: how to know if data is fabricated
by
noodle
▴ 570
> Can you clarify what you mean by "100% of reads pass cutadapt, even > though 70% of reads contain adapters and get trimmed. The header o…
Comment: Software to separate reads from different individuals
by
GenoMax
141k
If you have independent information available (e.g. genotype data for both individuals) then you *may* be able to assign reads based on the…
Answer: Extract protein sequence
by
Matthias Zepper
4.5k
You didn't mention what kind of organism you are working with and what kind of protein you are looking for? If it happens to be a microbia…
Comment: How to use limma to find differentially expressed genes in response to a continu
by
pairedttest
▴ 10
Thank you Gordon for your expertise. One question that I have now that I have a list of DE genes is how to interpret logFC of this continuo…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Yes I plan to use QIIME2, but I'm Cutadapting outside QIIME so its easier to MultiQC without importing/unzipping QZAs (and QIIME2 importing…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
GenoMax
141k
> 3' adapters were removed aprox. 90 times each one, so there sohuld not be read-through at all here Then you have data that has poor Q sc…
Comment: FastQC Quality per tile and per sequence behaving strange after using Cutadapt
by
salias
• 0
Following your advice, I checked the primer and adapters sequences and edited the question accordingly
Comment: How should I make kallisto indexes?
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dsull
★ 5.9k
We can't phase them out per se, because ``kallisto index`` is still the engine responsible for creating the index under the hood (and there…
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