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116,694 results • Page
1 of 2334
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0
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Telescope issue
Telescope
RNAseq
4 minutes ago by
eleven11
• 0
0
votes
0
replies
10
views
How to find overlap of clusters in two seurat porject
clustering
seurat
overlap
match
35 minutes ago by
J
• 0
3
votes
6
replies
265
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 hour ago by
me
▴ 760 • written 1 day ago by
Mariana
▴ 40
0
votes
0
replies
23
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
2 hours ago by
sarphilsar
• 0
0
votes
1
reply
45
views
Adjust pvalue in R with different approach give me all different outcome
statistics
pvalue
adjustment
R
updated 1 hour ago by
Aspire
▴ 300 • written 2 hours ago by
Jonathan Yoou
▴ 60
795
votes
167
replies
142k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
0
votes
1
reply
44
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
ram
storage
pssm
updated 2 hours ago by
GenoMax
141k • written 2 hours ago by
Nafi
• 0
0
votes
1
reply
33
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 1 hour ago by
GenoMax
141k • written 2 hours ago by
jeffrey.maurer.informatics
• 0
0
votes
0
replies
32
views
p-value in CIBERSORT
CIBERSORT
p-value
updated 2 hours ago by
Ram
43k • written 3 hours ago by
michelafrancesconi9
▴ 20
0
votes
2
replies
109
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 3 hours ago by
GenoMax
141k • written 9 hours ago by
Dora
▴ 10
0
votes
0
replies
52
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 3 hours ago by
Ram
43k • written 4 hours ago by
Chakri
• 0
0
votes
0
replies
50
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 2 hours ago by
Ram
43k • written 5 hours ago by
Ahiad Chen Zion
• 0
0
votes
4
replies
151
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 5 hours ago by
Michael
54k • written 6 hours ago by
Riccardo
▴ 10
0
votes
0
replies
47
views
barcode of TCR-sequencing
barcode
5 hours ago by
yueli7
▴ 250
0
votes
0
replies
53
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 5 hours ago by
Ram
43k • written 6 hours ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
50
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 4 hours ago by
Ram
43k • written 7 hours ago by
Alexandros
• 0
0
votes
1
reply
80
views
unable to get feature count results
featureCounts
updated 2 hours ago by
Ram
43k • written 7 hours ago by
Ravita
• 0
0
votes
0
replies
51
views
Subsetting and merging back Seurat Object brings different results
Seurat
7 hours ago by
Bine
▴ 60
0
votes
3
replies
108
views
KEGG Pathways
r
RNA-seq
updated 51 minutes ago by
Ram
43k • written 8 hours ago by
Sudip
• 0
4
votes
6
replies
3.8k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 8 hours ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
53
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
8 hours ago by
Bine
▴ 60
0
votes
1
reply
202
views
News:
FINAL CALL: 8th Berlin Summer School in NGS Data Analysis - Only a few last places available
DNA-seq
variant-calling
RNA-seq
illumina
transcriptomics
9 hours ago by
David Langenberger
11k
0
votes
0
replies
53
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
9 hours ago by
8armed
• 0
0
votes
1
reply
105
views
Deseq2
Deseq2
updated 10 hours ago by
Jack Tierney
▴ 360 • written 10 hours ago by
Sudip
• 0
1
vote
1
reply
131
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 10 hours ago by
Michael
54k • written 20 hours ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
172
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 10 hours ago by
Lluís R.
★ 1.2k • written 12 hours ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
107
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 11 hours ago by
ATpoint
82k • written 11 hours ago by
Sudip
• 0
1
vote
2
replies
126
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 2 hours ago by
Ram
43k • written 11 hours ago by
Ravita
• 0
0
votes
0
replies
46
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
11 hours ago by
Adyasha
• 0
0
votes
0
replies
50
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
14 hours ago by
fanglujing
▴ 60
0
votes
0
replies
66
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
17 hours ago by
Jacob
• 0
0
votes
3
replies
669
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 18 hours ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
176
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 13 hours ago by
Ram
43k • written 20 hours ago by
Hamtaro
▴ 50
0
votes
2
replies
159
views
Post-imputation plot
michigan-imputation-server
quality-control
5 hours ago by
kl
▴ 10
0
votes
1
reply
116
views
Differential Accessibility
DiffBind
updated 21 hours ago by
Ram
43k • written 21 hours ago by
Shloka
• 0
0
votes
3
replies
202
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 6 hours ago by
GenoMax
141k • written 22 hours ago by
kim
• 0
3
votes
2
replies
288
views
Extract protein sequence
fasta
alignment
blast
9 hours ago by
anna
▴ 20
3
votes
3
replies
239
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 1 day ago by
noodle
▴ 580 • written 1 day ago by
WUSCHEL
▴ 750
0
votes
1
reply
103
views
metagenomic virome quality assessment
viromics
metagenomics
updated 1 day ago by
Ram
43k • written 1 day ago by
Petchimuthu
• 0
3
votes
7
replies
233
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
1 day ago by
salias
• 0
0
votes
0
replies
73
views
Using limma in methylation EM-seq?
EM-seq
methylation
1 day ago by
Lluís R.
★ 1.2k
4
votes
7
replies
516
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
1 day ago by
e.r.zakiev
▴ 200
0
votes
0
replies
82
views
Synteny analysis
bacterial
synteny
genome
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Namil
• 0
0
votes
4
replies
181
views
Genbank File Format
gbkformat
10 hours ago by
alenew.am
• 0
0
votes
5
replies
336
views
How should I make kallisto indexes?
kallisto
updated 1 day ago by
dsull
★ 5.9k • written 15 days ago by
bioinfo
▴ 150
0
votes
0
replies
165
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
1 day ago by
SSSJec
• 0
0
votes
3
replies
174
views
Software to separate reads from different individuals
software
development
nanopore
updated 23 hours ago by
GenoMax
141k • written 1 day ago by
njornet
▴ 20
0
votes
0
replies
72
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
1 day ago by
David
• 0
4
votes
5
replies
244
views
High Malat-1 expression in single cell data
cell
analysis
single
updated 1 day ago by
dsull
★ 5.9k • written 1 day ago by
Kazo
▴ 10
0
votes
2
replies
140
views
How to update R on ubuntu
installation
update
R
apt-get
1 day ago by
Bosberg
▴ 50
116,694 results • Page
1 of 2334
Recent Votes
CTO/founding engineer role at Voyant Bio
Programmatically retrieving positions of protein active site residues
Programmatically retrieving positions of protein active site residues
A: Can Biopython Properly Import Fasta Headers With Spaces In Them?
Programmatically retrieving positions of protein active site residues
Answer: Polishing genome assembly
Answer: Integrate transcriptomic data and proteomics data.
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Recent Replies
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
▴ 300
- 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?
Comment: from row count to tpm
by
Ram
43k
Hi https://www.biostars.org/u/119503/ Why did you delete this post?
Comment: ERROR When Using Ensembl Plants Biomart Wget API
by
GenoMax
141k
A couple of hours back using `plants.ensembl.org` was generating a 504 error but it seems to be working now. wget -O result.txt 'http…
Comment: why renaming Idents in Seurat object doesn't work?
by
Assa Yeroslaviz
★ 1.8k
Don't understand this comment. I don't have any columns with this name.
Answer: ERROR When Using Ensembl Plants Biomart Wget API
by
Ben_Ensembl
★ 2.4k
Hi Dora, For plant species such as *A. thalina*, you should use the http://plants.ensembl.org/biomart service, so the start of your wget…
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