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970 results • Page
3 of 20
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Votes
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0
votes
1
reply
781
views
cnetplot category names are too long
clusterprofiler
RNA-Seq
enrichplot
cnetplot
updated 4 days ago by
Ram
43k • written 2.7 years ago by
carov
• 0
0
votes
1
reply
151
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated 4 days ago by
Ram
43k • written 5 days ago by
ernestine.kubi
• 0
0
votes
0
replies
106
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
5 days ago by
VITALA
• 0
1
vote
2
replies
251
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
4 days ago by
rianna.collins
• 0
0
votes
1
reply
184
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 5 days ago by
i.sudbery
19k • written 5 days ago by
Edmond
• 0
0
votes
0
replies
144
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
5 days ago by
O.rka
▴ 710
0
votes
1
reply
679
views
after selecting specific GO terms to plot, cneplot is not showing any color for genes, GO terms and only showing lines without nodes.
cneplot
updated 5 days ago by
Ram
43k • written 5 days ago by
Dr Huma Naz
• 0
2
votes
2
replies
274
views
p-value in CIBERSORT
CIBERSORT
p-value
5 days ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
373
views
Telescope issue
Telescope
RNA-seq
updated 5 days ago by
GenoMax
142k • written 5 days ago by
eleven11
• 0
5
votes
6
replies
524
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 6 days ago by
me
▴ 760 • written 7 days ago by
Mariana
▴ 40
1
vote
1
reply
232
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 5 days ago by
Ram
43k • written 6 days ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
290
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
5 days ago by
Nafi
• 0
1
vote
3
replies
281
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 5 days ago by
GenoMax
142k • written 6 days ago by
jeffrey.maurer.informatics
• 0
1
vote
3
replies
278
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
12 hours ago by
Dora
▴ 10
0
votes
0
replies
164
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 6 days ago by
Ram
43k • written 6 days ago by
Chakri
• 0
0
votes
1
reply
186
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated 4 days ago by
Adam
▴ 30 • written 6 days ago by
Ahiad Chen Zion
• 0
1
vote
5
replies
329
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
3 days ago by
Riccardo
▴ 10
0
votes
0
replies
137
views
barcode of TCR-sequencing
barcode
6 days ago by
yueli7
▴ 250
0
votes
0
replies
129
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 6 days ago by
Ram
43k • written 6 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
126
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 6 days ago by
Ram
43k • written 6 days ago by
Alexandros
• 0
0
votes
1
reply
174
views
unable to get feature count results
featureCounts
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
0
votes
3
replies
285
views
KEGG Pathways
r
RNA-seq
updated 5 days ago by
Ram
43k • written 6 days ago by
Sudip
• 0
4
votes
6
replies
3.9k
views
Taking the difference of two VCFs (or removing singletons)
genome
sequencing
singleton
SNP
filter
updated 6 days ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
133
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
6 days ago by
Bine
▴ 60
0
votes
1
reply
290
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
6 days ago by
David Langenberger
11k
0
votes
1
reply
189
views
Deseq2
Deseq2
updated 6 days ago by
Jack Tierney
▴ 360 • written 6 days ago by
Sudip
• 0
1
vote
1
reply
235
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 6 days ago by
Michael
54k • written 6 days ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
282
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 6 days ago by
Lluís R.
★ 1.2k • written 6 days ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
201
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 6 days ago by
ATpoint
82k • written 6 days ago by
Sudip
• 0
1
vote
2
replies
228
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 6 days ago by
Ram
43k • written 6 days ago by
Ravita
• 0
0
votes
2
replies
165
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
updated 4 hours ago by
GenoMax
142k • written 6 days ago by
Adyasha
• 0
0
votes
0
replies
116
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
6 days ago by
fanglujing
▴ 60
0
votes
0
replies
134
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
6 days ago by
Jacob
• 0
0
votes
3
replies
744
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 6 days ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
275
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 6 days ago by
Ram
43k • written 6 days ago by
Hamtaro
▴ 50
0
votes
1
reply
183
views
Differential Accessibility
DiffBind
updated 6 days ago by
Ram
43k • written 6 days ago by
Shloka
• 0
0
votes
3
replies
294
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 6 days ago by
GenoMax
142k • written 6 days ago by
kim
• 0
3
votes
2
replies
385
views
Extract protein sequence
fasta
alignment
blast
5 days ago by
anna
▴ 20
3
votes
3
replies
324
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 7 days ago by
noodle
▴ 580 • written 7 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
170
views
metagenomic virome quality assessment
viromics
metagenomics
updated 6 days ago by
Ram
43k • written 7 days ago by
Petchimuthu
• 0
3
votes
7
replies
348
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
6 days ago by
salias
• 0
0
votes
0
replies
126
views
Using limma in methylation EM-seq?
EM-seq
methylation
7 days ago by
Lluís R.
★ 1.2k
4
votes
7
replies
591
views
Very low RNA splicing rate for pulmonary AT2 cells
RNA-velocity
scVelo
scRNA-seq
splicing
7 days ago by
e.r.zakiev
▴ 210
0
votes
0
replies
125
views
Synteny analysis
bacterial
synteny
genome
updated 7 days ago by
GenoMax
142k • written 7 days ago by
Namil
• 0
0
votes
4
replies
263
views
Genbank File Format
gbkformat
6 days ago by
alenew.am
• 0
0
votes
5
replies
425
views
How should I make kallisto indexes?
kallisto
updated 6 days ago by
dsull
★ 6.0k • written 21 days ago by
bioinfo
▴ 150
0
votes
0
replies
233
views
Assist me in determining whether the analysis process using the limma package has been executed correctly
limma
ArrayExpress
DifferentialExpression
GEOquery
7 days ago by
SSSJec
• 0
0
votes
3
replies
220
views
Software to separate reads from different individuals
software
development
nanopore
updated 6 days ago by
GenoMax
142k • written 7 days ago by
njornet
▴ 20
0
votes
0
replies
94
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
7 days ago by
David
• 0
0
votes
2
replies
235
views
How to update R on ubuntu
installation
update
R
apt-get
7 days ago by
Bosberg
▴ 50
970 results • Page
3 of 20
Recent Votes
Comment: High Malat-1 expression in single cell data
A: Meme-Tools: Bit score
Meme-Tools: Bit score
Meme-Tools: Bit score
Comment: error in R code
DEXSeq multiple time points
How to find the most frequent alternative-splicing event from DEXSEQ data?
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Recent Awards •
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Popular Question
to
bhumm
▴ 140
Teacher
to
Matthias Zepper
4.6k
Popular Question
to
sidrah.maryam
▴ 50
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to
gubrins
▴ 290
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Recent Replies
Answer: Gene ontology and homologs
by
geneontologyhelp
▴ 390
No. Homology is defined as shared common ancestry. Two genes that take part in the same biological process may not have the same functio…
Answer: error in R code
by
Matthias Zepper
4.6k
I quickly googled [the source code of that function][1], and the error is triggered by this condition: if(length(wn) < 1 || !is.whol…
Comment: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
kalavattam
▴ 190
Thanks for the explanation. I noticed and corrected a typo in which "*read* reverse strand" initially read as "*mate* reverse strand" in t…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
It's a commercial product, a *Staphylococcus hominis* genome. This species is not found in the DADA2 results, so I guess DADA2 is not ident…
Comment: Question regarding WGCNA
by
Ram
43k
Plots are incomplete without legends. Please share the complete plot with mappings for shape and color.
Comment: Quetion regarding WGCNA
by
deepak
• 0
Thank you for your reply andres.firrincieli. I have attached the PCA plot of the expression data used in the WGCNA. ![enter imag…
Comment: Design matrix Differential expression analysis
by
SHN
▴ 40
Got it, thank you for your response. SN
Comment: How to interpret DEXseq results in therms of significance
by
Sara
▴ 30
Hi, I used write.table(as.data.frame(DEXSeqResults(MyObj)), "Results.tsv", quote=FALSE, sep="\t", dec=".") to save the result but I recei…
Comment: Tissue-specific DEG analysis with DEseq2
by
M.
▴ 30
Can I ask what do you exactly mean by same experiment? If you are talking about the same donor and the same procedure, unfortunately, not a…
Comment: install package: package ‘gmwm’ is not available for this version of R
by
Ram
43k
Find someone with computer skills near you and consult them. From your posts on the forum, it's clear that you need help at a level that we…
Comment: Gene Specific coverage from WGS data
by
GenoMax
142k
This is not going to work no matter what program you use since the chromosome identifiers in your GTF (`MN908947.3 `) do not match your BA…
Comment: install.packages("imudata") - package ‘imudata’ is not available for this versio
by
Ram
43k
Read the answers in the post, understand them and try to implement them.
Comment: High Malat-1 expression in single cell data
by
t.montserrat.ayuso
▴ 10
Just using the normalized expression of Malat1 works.
Comment: Can I merge Hi-C fastq files from different lanes?
by
Winter
• 0
Awesome, thank you for the concise and straight-forward answer!
Comment: error in R code
by
ATpoint
82k
Look, before you keep posting these sorts of questions and might gross of users, please read and follow https://www.biostars.org/p/357878/ …
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