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116,700 results • Page
1 of 2334
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0
votes
1
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91
views
How to find overlap of clusters in two seurat porject
clustering
seurat
updated 10 minutes ago by
Adam
▴ 30 • written 1 day ago by
J
• 0
1
vote
2
replies
131
views
DESeq2 processing problems
deseq2
R
updated 14 minutes ago by
Adam
▴ 30 • written 10 hours ago by
jagdish7921
• 0
1
vote
2
replies
35
views
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
43 minutes ago by
nicole.kavanagh
• 0
0
votes
1
reply
677
views
cnetplot category names are too long
RNASeq
clusterprofiler
cnetplot
enrichplot
updated 1 hour ago by
bkleiboeker
▴ 370 • written 2.7 years ago by
carov
• 0
0
votes
1
reply
30
views
Mutect2 for mitochondria variant discovery
mutect2
mitochondria
updated just now by
Ram
43k • written 1 hour ago by
ernestine.kubi
• 0
0
votes
0
replies
22
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
2 hours ago by
VITALA
• 0
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
124
views
POSSUM not working due to incompatible pssm file
fasta
pse-pssm
pssm
POSSUM
updated 13 hours ago by
Ram
43k • written 16 hours ago by
rianna.collins
• 0
0
votes
1
reply
104
views
Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
rna-seq
updated 7 hours ago by
i.sudbery
19k • written 18 hours ago by
Edmond
• 0
0
votes
0
replies
80
views
What open-source tools can determine the coverage/completion of a pathway based on EC numbers?
metagenomics
metacyc
enzyme
pathway
genomics
18 hours ago by
O.rka
▴ 710
0
votes
1
reply
238
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 13 hours ago by
Ram
43k • written 18 hours ago by
Dr Huma Naz
• 0
2
votes
2
replies
193
views
p-value in CIBERSORT
CIBERSORT
p-value
8 hours ago by
michelafrancesconi9
▴ 20
0
votes
5
replies
237
views
Telescope issue
Telescope
RNA-seq
updated 1 hour ago by
GenoMax
141k • written 23 hours ago by
eleven11
• 0
5
votes
6
replies
424
views
Programmatically retrieving positions of protein active site residues
Uniprot
PDB
Proteins
updated 1 day ago by
me
▴ 760 • written 2 days ago by
Mariana
▴ 40
0
votes
0
replies
94
views
Defined objects of type "S4" error in single cell analysis
Seurat
single-cell
DoubletFinder
single-nuclei
SeuratObject
1 day ago by
sarphilsar
• 0
1
vote
1
reply
163
views
Adjust pvalue in R with different approach give me all different outcome
statistics
R
p-value
updated 20 hours ago by
Ram
43k • written 1 day ago by
Jonathan Yoou
▴ 60
1
vote
2
replies
208
views
Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x64-linux
blast
pssm
5 hours ago by
Nafi
• 0
1
vote
3
replies
211
views
What does 'bundle_uuid' refer to in this metadata sheet?
SRA
illumina
GEO
metadata
updated 21 hours ago by
GenoMax
141k • written 1 day ago by
jeffrey.maurer.informatics
• 0
0
votes
2
replies
166
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
updated 1 day ago by
GenoMax
141k • written 1 day ago by
Dora
▴ 10
0
votes
0
replies
113
views
News:
Goodbye, Slow Code? How BioNumpy can Redefine Python’s Role in Bioinformatics!
BioNumPy
Python
NumPy
updated 1 day ago by
Ram
43k • written 1 day ago by
Chakri
• 0
0
votes
1
reply
97
views
RNA editing sites based on DNA seq and RNA seq
RNA-editing
updated just now by
Adam
▴ 30 • written 1 day ago by
Ahiad Chen Zion
• 0
0
votes
4
replies
212
views
Introduce SNPs on FASTA
simulation
snps
haplotypes
pharmacogenetics
updated 1 day ago by
Michael
54k • written 1 day ago by
Riccardo
▴ 10
0
votes
0
replies
88
views
barcode of TCR-sequencing
barcode
1 day ago by
yueli7
▴ 250
0
votes
0
replies
91
views
News:
Online course: Meta-analysis in R - last 2 seats left
Meta-Analysis
Statistics
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
88
views
Somatic variant calling with Mutect2 using 2 matched-normals for one sample
cancer
mutect
variant-calling
GATK
somatic-variants
updated 1 day ago by
Ram
43k • written 1 day ago by
Alexandros
• 0
0
votes
1
reply
121
views
unable to get feature count results
featureCounts
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
0
replies
87
views
Subsetting and merging back Seurat Object brings different results
Seurat
1 day ago by
Bine
▴ 60
0
votes
3
replies
225
views
KEGG Pathways
r
RNA-seq
updated 1 day ago by
Ram
43k • written 1 day 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 1 day ago by
Andres
▴ 20 • written 9.6 years ago by
hermathena
▴ 40
0
votes
0
replies
92
views
Seurat object reductions (PCA, UMAP,..) after subsetting data
Seurat
1 day ago by
Bine
▴ 60
0
votes
1
reply
242
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
1 day ago by
David Langenberger
11k
0
votes
0
replies
96
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
1 day ago by
8armed
• 0
0
votes
1
reply
145
views
Deseq2
Deseq2
updated 1 day ago by
Jack Tierney
▴ 360 • written 1 day ago by
Sudip
• 0
1
vote
1
reply
177
views
Polishing genome assembly
polishing
Nanopore
PacBio
updated 1 day ago by
Michael
54k • written 1 day ago by
Lissa Cruz Saavedra
• 0
5
votes
3
replies
219
views
6 follow
Integrate transcriptomic data and proteomics data.
OMICS
updated 1 day ago by
Lluís R.
★ 1.2k • written 1 day ago by
이민경[학생](대학원 융합의과학과)
• 0
2
votes
2
replies
153
views
MA plot of shrunken fold change
MA-plot
Deseq2
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Sudip
• 0
1
vote
2
replies
181
views
Need help for downloading arabdopsis thaliana reference genome fasta file and gtf file
Arabidopsis-thaliana
gtf
reference-genome
updated 1 day ago by
Ram
43k • written 1 day ago by
Ravita
• 0
0
votes
0
replies
84
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
1 day ago by
Adyasha
• 0
0
votes
0
replies
87
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
1 day ago by
fanglujing
▴ 60
0
votes
0
replies
103
views
Are some metagenomes too complex for MAGs?
metagenomics
metagenome
MAGs
assembly
1 day ago by
Jacob
• 0
0
votes
3
replies
706
views
Why cd-hit-est not work when sequence identity threshold<0.95?
genome
cluster
sequence
updated 1 day ago by
weidonglu
• 0 • written 21 months ago by
JZX
• 0
0
votes
4
replies
218
views
Perfom a Gene Ontology Analysis from GO terms txt file
RNA-Seq
GO
updated 1 day ago by
Ram
43k • written 1 day ago by
Hamtaro
▴ 50
0
votes
4
replies
278
views
Post-imputation plot
michigan-imputation-server
quality-control
5 hours ago by
kl
▴ 10
0
votes
1
reply
151
views
Differential Accessibility
DiffBind
updated 1 day ago by
Ram
43k • written 1 day ago by
Shloka
• 0
0
votes
3
replies
245
views
Landmark gene selection in L1000.
L1000
landmark-gene
cmap
updated 1 day ago by
GenoMax
141k • written 1 day ago by
kim
• 0
3
votes
2
replies
335
views
Extract protein sequence
fasta
alignment
blast
22 hours ago by
anna
▴ 20
3
votes
3
replies
286
views
Is it possible to bulk download files from GEO repository?
RNA-seq
Galaxy
Tanscriptomics
updated 2 days ago by
noodle
▴ 580 • written 2 days ago by
WUSCHEL
▴ 750
0
votes
1
reply
145
views
metagenomic virome quality assessment
viromics
metagenomics
updated 2 days ago by
Ram
43k • written 2 days ago by
Petchimuthu
• 0
3
votes
7
replies
283
views
FastQC Quality per tile and per sequence behaving strange after using Cutadapt
fastqc
cutadapt
illumina
tile
paired-end
2 days ago by
salias
• 0
0
votes
0
replies
110
views
Using limma in methylation EM-seq?
EM-seq
methylation
2 days ago by
Lluís R.
★ 1.2k
116,700 results • Page
1 of 2334
Recent Votes
Comment: Adjust pvalue in R with different approach give me all different outcome
Comment: Bacterial plasmid analysis
Comment: DESeq2 processing problems
Comment: What does 'bundle_uuid' refer to in this metadata sheet?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
What Is The Difference Between Structural Variants (Svs) And Copy-Number Variants (Cnvs)?
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
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Recent Replies
Answer: How to find overlap of clusters in two seurat porject
by
Adam
▴ 30
I think your best bet would be to use annotation mapping. You can use the features of your clusters in group 1 and apply them to group 2 to…
Answer: DESeq2 processing problems
by
Adam
▴ 30
> when I put in the dataset, I am not able to run it for DEG analysis because system asks me to remove the first column which is of gene na…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Thank you so much for your quick response, I have been searching scientific papers for about a week but have failed to come up with a reaso…
Comment: Bacterial plasmid analysis
by
GenoMax
141k
> however I'm not sure this would be appropriate in my case as the plasmid sequences are obviously much more diverse and vary in size Can…
Answer: cnetplot category names are too long
by
bkleiboeker
▴ 370
I'm sure someone could find a more elegant solution using `stringr::str_wrap`, but for a one-time solution I did this: # my results of…
Comment: Telescope issue
by
GenoMax
141k
You could edit the SAM file but I wonder if this problem is present in your original fastq data file so if not inconvenient do the alignmen…
Comment: Mutect2 for mitochondria variant discovery
by
GenoMax
141k
> I keep getting error. Without providing information about the actual error no one can help. Please edit the post and add this informati…
Comment: Telescope issue
by
eleven11
• 0
Thank you! how would I correct that?
Comment: DESeq2 processing problems
by
Ram
43k
This is an open science community, not a place to write an email to Michael Love. Please address the entire community.
Comment: Post-imputation plot
by
kl
▴ 10
All of them are G/C and A/T variants Some seem mismatches based on AF and some seem to need flipping. I guess I am confused, as in the Mich…
Comment: Minimum RAM and Storage requirement for creating PSSM using ncbi-blast-2.2.30+-x
by
Nafi
• 0
Thank you for the reply I have 16 gb of RAM then I can give a try then.
Comment: Alternatives to metanalyisis. P integration. Horiztonal integration RNA-seq
by
i.sudbery
19k
Can you give more details of the data you are planning to use. What is the different studies, what are the comparisons you want to make.
Comment: p-value in CIBERSORT
by
michelafrancesconi9
▴ 20
Thank you so much!!
Comment: POSSUM not working due to incompatible pssm file
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
Comment: after selecting specific GO terms to plot, cneplot is not showing any color for
by
Ram
43k
Please use the formatting bar (especially the `code` option) to present your post better. You can use backticks for inline code (\`text\` b…
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