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113,847 results • Page
1 of 2277
Sort: Rank
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Votes
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0
votes
0
replies
7
views
R script in docker
R
Visual_studio_code
Docker
6 minutes ago by
mrashad
▴ 70
0
votes
1
reply
23
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 46 minutes ago by
colindaven
5.7k • written 50 minutes ago by
CTLong
▴ 10
0
votes
0
replies
12
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
1 hour ago by
maxlaubstein
• 0
0
votes
1
reply
15
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
updated just now by
Pierre Lindenbaum
158k • written 1 hour ago by
J
• 0
0
votes
3
replies
98
views
ERROR FILE EXTENSION
Prokka
2 hours ago by
syirah4
• 0
0
votes
1
reply
83
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
updated 2 hours ago by
Tao
▴ 30 • written 12 hours ago by
Bryan
▴ 10
0
votes
6
replies
252
views
Where is the index command?
samtools
updated 5 hours ago by
GenoMax
136k • written 12 hours ago by
luque007
• 0
0
votes
0
replies
58
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
10 hours ago by
luckyday1661
• 0
0
votes
1
reply
92
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 9 hours ago by
bk11
★ 1.8k • written 10 hours ago by
synat.keam
▴ 80
0
votes
0
replies
51
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
11 hours ago by
DINESHR
• 0
772
votes
164
replies
128k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
1
vote
1
reply
119
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 11 hours ago by
rpolicastro
12k • written 11 hours ago by
newbee
▴ 40
0
votes
0
replies
67
views
deeptools k-means clustering
heatmap
deeptools
chipseq
12 hours ago by
biology_inform
▴ 50
0
votes
0
replies
60
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
14 hours ago by
tss243
• 0
3
votes
6
replies
318
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 15 hours ago by
NextGenSeek
• 0 • written 1 day ago by
singhankit973
• 0
0
votes
2
replies
137
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 16 hours ago by
GenoMax
136k • written 16 hours ago by
JACKY
▴ 120
0
votes
0
replies
79
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
16 hours ago by
aheinzel
▴ 130
3
votes
3
replies
152
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 6 hours ago by
Jeremy
▴ 840 • written 17 hours ago by
ohtang7
▴ 40
0
votes
0
replies
61
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 16 hours ago by
GenoMax
136k • written 17 hours ago by
sativus
▴ 10
0
votes
0
replies
73
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 18 hours ago by
GenoMax
136k • written 18 hours ago by
PierreGT
• 0
5
votes
5
replies
370
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 16 hours ago by
i.sudbery
18k • written 1 day ago by
sehriban.buyukkilic
• 0
0
votes
0
replies
75
views
sequencing deep mutational scanning library
mutagenesis
illumina
long-read
sequencing
18 hours ago by
reaset41
• 0
0
votes
4
replies
189
views
Making multiple box plots with relative abundance in R
R
Boxplots
17 hours ago by
ohtang7
▴ 40
1
vote
1
reply
124
views
Two identical reads in my bam files but with a different in CIGAR are mapped in a different location in IGV
pysam
19 hours ago by
ManuelDB
▴ 80
0
votes
0
replies
61
views
GMT file from eggnog annotation
gmt
annotation
Eggnog
19 hours ago by
jorge.cortes.miranda
• 0
4
votes
7
replies
232
views
regarding blast result interpretation
blast
updated 18 hours ago by
dthorbur
▴ 880 • written 20 hours ago by
Raman
• 0
2
votes
3
replies
169
views
Blastn DB issue
cgmlst
blastn
updated 5 hours ago by
Philipp Bayer
8.1k • written 22 hours ago by
hakhasan
• 0
0
votes
2
replies
142
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
1 hour ago by
eamaunders
• 0
1
vote
2
replies
172
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 23 hours ago by
DBScan
▴ 210 • written 1 day ago by
applepie
• 0
0
votes
1
reply
323
views
FVA on Sybil
R
Sybil
metabolic
fba
fva
updated 1 day ago by
Thomas
• 0 • written 22 months ago by
isM15
• 0
0
votes
3
replies
227
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
9 hours ago by
cook.675
▴ 200
0
votes
1
reply
135
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 20 hours ago by
rpolicastro
12k • written 1 day ago by
saipra003
▴ 10
0
votes
0
replies
91
views
How to find node Postion and source(sample) ?
vg
1 day ago by
zhang yi xing
▴ 20
0
votes
4
replies
262
views
CHIPSEQ : Cut AND Run , DiffBind Parameters
Cut-Run
DiffBind
ChIP-seq
11 hours ago by
DINESHR
• 0
0
votes
0
replies
87
views
MUSCLE Protein Alignment of Distantly Related Proteins
muscle
protein
alignment
1 day ago by
Richard Fontaine
• 0
4
votes
6
replies
319
views
bwa mem hangs after a few thousand reads
bwa-mem
alignment
bwa
calling
variant
11 hours ago by
cee28
▴ 30
1
vote
1
reply
152
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 19 hours ago by
rpolicastro
12k • written 1 day ago by
O.rka
▴ 710
2
votes
2
replies
440
views
Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when pivoting from wide to long format
rnaseq
pivot_longer
ggplot2
updated 1 day ago by
cmdcolin
★ 3.4k • written 1 day ago by
Dylan C-C
• 0
3
votes
4
replies
270
views
Plotting a pvalue threshold for an FDR corrected pvalue <.05 when thats not present in R
FDR
volcano
plotting
R
plot
updated 23 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
RNAseqer
▴ 250
0
votes
1
reply
138
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 1 day ago by
ATpoint
78k • written 1 day ago by
ahonya
• 0
0
votes
0
replies
129
views
Bcftools consensus when reference is a deletion
consensus
vcf
1 day ago by
selplat21
▴ 20
1
vote
1
reply
178
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 1 day ago by
singh.vijender
▴ 100 • written 1 day ago by
DareDevil
★ 3.3k
0
votes
5
replies
309
views
How to deeply sequence long inserts
NGS
phage
read
display
Long
updated 23 hours ago by
GenoMax
136k • written 1 day ago by
Ryan
• 0
0
votes
1
reply
130
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 1 day ago by
singh.vijender
▴ 100 • written 1 day ago by
reza
▴ 300
0
votes
2
replies
197
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
1 day ago by
harter-ainsworth.izaak
• 0
0
votes
0
replies
96
views
scVelo cell transitions from marker gene expressing cells
velocity
scvelo
RNA
1 day ago by
rbronste
▴ 420
3
votes
2
replies
179
views
Moving AF tag to new column in a VCF file
mutect2
vcf
1 day ago by
Christian
▴ 30
1
vote
4
replies
258
views
How can I map coordinates between two strains of yeast?
coordinates
yeast
genome
mapping
fasta
updated 1 day ago by
GenoMax
136k • written 2 days ago by
Jimmy
▴ 10
0
votes
1
reply
149
views
The difference blastn output when using subject and db options
genome
blastn
mite
annotation
tracker
updated 1 day ago by
GenoMax
136k • written 1 day ago by
praasu
▴ 40
1
vote
3
replies
244
views
Identify clusters of populations based on gene expression
Seq
Single
cell
RNA
updated 1 day ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
Bine
▴ 50
113,847 results • Page
1 of 2277
Recent Votes
Answer: BULK mRNA-seq with UMIs. Do I need to normalize by gene length?
BULK mRNA-seq with UMIs. Do I need to normalize by gene length?
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
Comment: Using ggplot2 to make barplots of RNASeq data - maintaining sample metadata when
How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
Comment: scRNA-seq: Consistent low number of cells and low fraction reads across the samp
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▴ 100
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Recent Replies
Answer: Is bisulfite-seq data from different studies comparable with each other?
by
colindaven
5.7k
Probably not. Batch effects are a huge issue so read up on the statistical literature. You can try, but be very skeptical. Start with he…
Comment: How can I amend the output of a DIAMOND python script?
by
eamaunders
• 0
wow, that was 1 million times easier than what I was attempting! Thanks Nitin.
Comment: ERROR FILE EXTENSION
by
syirah4
• 0
It pop out error: file existence/permissions problem in trying to open CM file. I can't upload the picture here
Answer: ERROR FILE EXTENSION
by
Tao
▴ 30
Perhaps you can install it using canda, or you can see the official documentation.[Prokka][1] [1]: https://github.com/tseemann/prokka
Answer: filtering SAM/BAM to remove hits spanning short combined alignment lengths and l
by
Tao
▴ 30
Use the python package pysam [pysam document][1] [1]: https://readthedocs.org/projects/pysam/
Comment: ERROR FILE EXTENSION
by
Mensur Dlakic
★ 25k
Tough to troubleshoot without exact installation command, exact setup command, and exact error message.
Comment: Blastn DB issue
by
Philipp Bayer
8.1k
Yeah it scares me!!! I am running many BLASTs for many mitogenomes at the moment. There are many highly similar sequence hits on NT across …
Comment: Where is the index command?
by
GenoMax
136k
Please accept @Michael's answer (green check mark) to provide closure to this thread.
Comment: Where is the index command?
by
luque007
• 0
**ran the index with sudo and it worked !!!**
Comment: Where is the index command?
by
luque007
• 0
samtools index ran but returned samtools index: failed to create or write index I will look for solution to that Progress made!!!
Comment: Where is the index command?
by
luque007
• 0
ran sudo apt update (never used this windows ubuntu before) Holy Hell 111 updateable Ran sudo apt-get update && sudo apt-get upgrad…
Comment: htShinyExample-5.3 - not working
by
Ram
41k
Show us the exact code you’re using or at least as much of it as you can. Also, who’s “we” and “us”?
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
Jeremy
▴ 840
I agree with ATpoint - you can replace 0s with .1. For determining skewness, I like to use the skewness() function in the moments package …
Comment: Where is the index command?
by
luque007
• 0
Thanks for comment on root. This is ubuntu running in windows and I had not yet set a user account (and added to sudoers) The error I get …
Comment: Viral genes not showing up in combined mouse+virus alignment
by
cook.675
▴ 200
I figured it out! The GTF.featureType uses 'exon' by default which is present in the mouse GTF but the viral GTF file has no exon feature n…
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