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19,194 results • Page
1 of 384
Sort: Rank
Rank
Views
Votes
Replies
0
votes
0
replies
11
views
Adjust Y axis scale in ggplot2
log
Y
axis
ggplot2
scale
21 minutes ago by
santiagoboccardo31
• 0
0
votes
1
reply
19
views
stat analysis
3
by
table
statistics
2
updated 22 minutes ago by
Pierre Lindenbaum
144k • written 44 minutes ago by
Rob
▴ 120
1
vote
1
reply
30
views
Copy Number Variations in Whole Exome Sequencing
WES
CNV
galaxy
germline
updated 1 hour ago by
Pierre Lindenbaum
144k • written 2 hours ago by
victorrg
• 0
0
votes
1
reply
17
views
Job:
Post-Doc in Plant Genomics
Resistance
Assembly
Weeds
Post-Doc
Annotation
updated 50 minutes ago by
Ram
36k • written 1 hour ago by
Eric
• 0
0
votes
2
replies
41
views
Why some primers in 'graphical view of primers' in the NCBI are represented as thicker lines?
NCBI
pick-PRIMERS
21 minutes ago by
Gerardo
• 0
1
vote
4
replies
35
views
"NaN " values are copied instead of float values (pd dataframe to adata.obs)
pandas
anndata
updated 46 minutes ago by
Ram
36k • written 2 hours ago by
akilabioinfo
▴ 10
0
votes
0
replies
21
views
Obtain equivalent variant ids (chr-pos-ref-alt) for GRCh37 and GRCh38
id
liftover
variant
2 hours ago by
fla28
• 0
0
votes
0
replies
37
views
Core/pan genome pipeline
pangenome
coregenome
mtdna
ngs
Nanopore
3 hours ago by
schulpen_91
• 0
0
votes
0
replies
23
views
Change parameter for unique genes in roary pangenome reconstruction from default values
roary
3 hours ago by
Priya
▴ 20
0
votes
0
replies
27
views
Retrieving starting/ending base cordinates and orientations of genes from TAIR using R
org.At.tair.db
R
Arabidopsis
3 hours ago by
ktm
• 0
0
votes
4
replies
109
views
Problem with BWA MEM
alignment
3 hours ago by
sihak
• 0
0
votes
2
replies
73
views
Strandedness of RNA-seq results
dual-RNA-seq
featurecounts
strandedness
HISAT2
updated 35 minutes ago by
Trivas
▴ 180 • written 4 hours ago by
jamesymtang
• 0
2
votes
5
replies
112
views
Difference in total gene counts between samples
rna-seq
3 hours ago by
bart
▴ 20
1
vote
4
replies
134
views
snakemake error - one of the commands exited with non-zero exit code
blastp
snakemake
updated 2 hours ago by
dariober
13k • written 8 hours ago by
Jonathan Yoou
▴ 50
25
votes
19
replies
5.8k
views
10 follow
Tool:
pathfindR - Enrichment Analysis using Active Subnetworks
enrichment
pathway
active
subnetwork
R
Tool
updated 6 hours ago by
Deepblue
▴ 10 • written 4.2 years ago by
egeulgen
★ 1.2k
666
votes
160
replies
83k
views
98 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
tutorial
News
handbook
updated 4 weeks ago by
Biostar
710 • written 5.4 years ago by
Istvan Albert
93k
0
votes
4
replies
241
views
How can I download from NCBI site assembly for specific genes involve in mRNA processing?
NCBI
download
assembly
6 hours ago by
dshdixit
▴ 10
1
vote
3
replies
72
views
ACGT101-miR program
sequenced
Adapter
trimming
miRNA
bioinformatics
data
updated 6 hours ago by
Michael Dondrup
51k • written 6 hours ago by
mahla.krishan
• 0
0
votes
1
reply
79
views
data correaltion
correlation
deseq2
prediction
R
target
updated 6 hours ago by
Michael Dondrup
51k • written 7 hours ago by
roniozagam94
• 0
3
votes
0
replies
84
views
Herald:
The Biostar Herald for Monday, May 16, 2022
herald
7 hours ago by
Biostar
710
0
votes
0
replies
49
views
Job:
Postdoctoral Fellowship Opening in Alzheimers Disease Genetics
Alzheimers
Postdoctoral
Genetics
Fellowship
8 hours ago by
vanessa
▴ 10
0
votes
7
replies
274
views
Basic python loop for paired fastq files
python
loop
updated 30 minutes ago by
Trivas
▴ 180 • written 4 days ago by
rescueson
• 0
3
votes
2
replies
86
views
Why divide by the root n when constructing the u statistic
statictic
t-test
u-test
t
offtopic
6 hours ago by
a661881
▴ 30
2
votes
6
replies
81
views
Saving file as .vcf
VCF
format
sequencing
files
Variant
call
NGS
data
updated 3 hours ago by
Ram
36k • written 9 hours ago by
Maryam
• 0
0
votes
2
replies
172
views
Enrichment analysis and GSEA
GSEA
EnrichmentAnalysis
updated 9 hours ago by
Mohammad Rezaei
▴ 20 • written 1 day ago by
amrsalaheldin50
• 0
3
votes
16
replies
6.7k
views
featureCounts: 0% successfully assigned fragments on multiple PE .BAM files
featureCounts
Rsubread
updated 9 hours ago by
KMS
• 0 • written 3.7 years ago by
imesi
▴ 20
0
votes
3
replies
130
views
VEP Could not get current species list - using predefined list instead
Ensembl
VEP
updated 5 hours ago by
Ben_Ensembl
★ 2.0k • written 10 hours ago by
Filago
▴ 90
0
votes
0
replies
49
views
Update column on selectInput in DT data table Shiny
shinywidgets
R
RShiny
9 hours ago by
abseq
• 0
0
votes
1
reply
73
views
How to Extract Values for SNPs by each chromosome and position using --window
plink
updated 8 hours ago by
Pierre Lindenbaum
144k • written 10 hours ago by
Raju
• 0
1
vote
5
replies
238
views
How to convert strand specific RNASEQ bam to bigwig
bamcoverage
RNASEQ
STrand
specific
updated 8 hours ago by
Carlo Yague
8.1k • written 4 days ago by
a.bafna
• 0
0
votes
0
replies
41
views
DBD::mysql required for VEP installation?
VEP
Perl
10 hours ago by
Filago
▴ 90
4
votes
2
replies
134
views
Question about a public scRNA dataset(single end)?
publicdataset
scRNA
singlecell
9 hours ago by
soda
▴ 40
2
votes
4
replies
162
views
can i take promoter upstream 2kb from tss ?
upstream
promoter
2kb
tss
updated 2 hours ago by
miles.thorburn
▴ 150 • written 15 hours ago by
isha.lily20
▴ 10
0
votes
3
replies
165
views
InteractiveComplexHeatmap on DESeq2 object with more than 2 groups
DESeq2
InteractiveComplexHeatmap
heatmap
updated 4 hours ago by
jared.andrews07
★ 13k • written 1 day ago by
miccoli.andrea89
• 0
0
votes
0
replies
91
views
Open issues in protein simulation in MC?
protein
protein-structure
protein-structure-prediction
22 hours ago by
user366312
▴ 10
0
votes
2
replies
153
views
Comparing expression of DEG gene in samples
DEG
limma
R
gene
2 hours ago by
Maryam
• 0
2
votes
4
replies
181
views
PCA to find clusters in gene expression data
expression
clustering
PCA
updated 1 day ago by
ATpoint
60k • written 1 day ago by
Hashirama
▴ 20
0
votes
3
replies
121
views
Genes mutations in cancer
GSEA
cancer
analysis
enrichment
updated 1 day ago by
Vincent Laufer
★ 1.8k • written 1 day ago by
amrsalaheldin50
• 0
0
votes
3
replies
122
views
Extract bed file of uwanted chromosome names and positions from bam file
bedfile
samtools
bamfile
updated 1 day ago by
Pierre Lindenbaum
144k • written 1 day ago by
tien
• 0
0
votes
1
reply
116
views
CNV loss and high expression
Copy
expression
number
updated 1 day ago by
iraun
★ 4.3k • written 1 day ago by
Kasthuri
▴ 290
4
votes
1
reply
115
views
Is it okay to map reads from WES designed for GRCh37 to GRCh38?
exome
whole
sequencing
updated 1 day ago by
Pierre Lindenbaum
144k • written 1 day ago by
samuelandjw
▴ 210
0
votes
0
replies
73
views
choose databbases in variant annotation
annotate
Annovar
1 day ago by
arwa.ahmad95
• 0
0
votes
1
reply
181
views
Which pipeline to choose for RNA velocity
Seurat
genomics
seq
velocity
RNA
10x
scRNA
updated 1 day ago by
rpolicastro
8.1k • written 1 day ago by
Meghamsh
• 0
2
votes
5
replies
143
views
agilent human all exon sureselct v7 bed file
exon
human
bed
v7
agilent
all
sureselect
updated 2 hours ago by
Kevin Blighe
81k • written 1 day ago by
soheil
• 0
4
votes
6
replies
237
views
Difference between commands [bowtie2, samtools]
bowtie2
samtools
updated 1 day ago by
iraun
★ 4.3k • written 1 day ago by
Jimpix
• 0
0
votes
3
replies
139
views
Mirdeep not giving results.
novel
Mirdeep
miRNA
sequence
RNA
updated 10 hours ago by
Michael Dondrup
51k • written 1 day ago by
A. Blue
• 0
0
votes
1
reply
122
views
mkdir: cannot create directory ‘/home/neel@m95/Desktop/AMR/cgview_comparison_tool/cog_db’: Permission denied
CGView
CCT
updated 1 day ago by
cpad0112
20k • written 1 day ago by
Neel
• 0
0
votes
2
replies
285
views
Is it correct to use Tophat2 directly followed by Cuffquant to only align to the reference transcriptomes without wishing to assemble new transcripts?
Tophat2
Cuffquant
Cufflinks
1 day ago by
zoukai3412085
• 0
0
votes
2
replies
130
views
minimum number of protein sequences for a sequence logo
logo
1 day ago by
Stefano
• 0
2
votes
1
reply
1.1k
views
How to choose threshold for filtering low counts before Voom transformation?
RNA-Seq
R
limma
voom
updated 1 day ago by
Gordon Smyth
★ 4.4k • written 21 months ago by
ihc.europa
▴ 20
19,194 results • Page
1 of 384
Recent Votes
Answer: Copy Number Variations in Whole Exome Sequencing
Comment: "NaN " values are copied instead of float values (pd dataframe to adata.obs)
Is a compositional bias in Sequence Content of initial bases in WES reads normal?
A: Error in (function...) thrown by WGCNA tutorial (R)
Comment: Issue with trend line and confidence interval
Answer: Correlating DNA methylation beta values with Gene expression levels (RNA-seq)
Why divide by the root n when constructing the u statistic
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Recent Replies
Comment: Why some primers in 'graphical view of primers' in the NCBI are represented as t
by
Gerardo
• 0
In this particularly case it appears after I click in "You can re-search for specific primers by accepting some of the unintended targets, …
Comment: stat analysis
by
Pierre Lindenbaum
144k
https://stats.stackexchange.com/questions/350466/
Comment: Basic python loop for paired fastq files
by
Trivas
▴ 180
Alternatively, and I think scales better depending on what else a pipeline entails, is to loop through a list of the root names, eg ["SRA1"…
Comment: Strandedness of RNA-seq results
by
Trivas
▴ 180
Agree with rpolicastro to post your mapping command. What's your sequencing structure (eg paired-end or single-end)?
Comment: Post-Doc in Plant Genomics
by
Ram
36k
Your posting link is broken - please fix it. Also, add the institute name and location to the title.
Comment: "NaN " values are copied instead of float values (pd dataframe to adata.obs)
by
Ram
36k
Follow cpad0112's advice. In the meantime, please do not paste screenshots of plain text content, it is counterproductive. You can copy pas…
Answer: Copy Number Variations in Whole Exome Sequencing
by
Pierre Lindenbaum
144k
> realised that most tools I'll be working on are available at Galaxy. and most tools you need are available on the linux command line.…
Comment: Why some primers in 'graphical view of primers' in the NCBI are represented as t
by
Mensur Dlakic
★ 18k
All of them happen to be at the same level, yet I admire that you noticed it at all. I am guessing it is a rendering artifact.
Comment: "NaN " values are copied instead of float values (pd dataframe to adata.obs)
by
cpad0112
20k
please post some example data from both the data frames. check the dtype of the dataframe esp FDR column in each of the data frame.
Comment: "NaN " values are copied instead of float values (pd dataframe to adata.obs)
by
akilabioinfo
▴ 10
I have done that too!! its not working. I couldnt able to copy from my metadata to anndata adata.obs(returns NAN values)
Comment: "NaN " values are copied instead of float values (pd dataframe to adata.obs)
by
Ram
36k
"Join" the data using a matching column instead of doing this blind assignment operation.
Comment: plink bim file stops at chrM
by
rturba
▴ 10
Hi, @chrchang523. I went to check my VCF file and I've noticed that after my chrM I had renamed my chrUn as 0 while my reference file had i…
Comment: can i take promoter upstream 2kb from tss ?
by
miles.thorburn
▴ 150
I don't work on plants so I don't know what the regulatory landscape is like, but you can find orthologs and some regulatory annotations on…
Comment: Comparing expression of DEG gene in samples
by
Maryam
• 0
Well I took a quick look at limma and adgeR in doing 'Differentially Expressed Genes' but I did not read carefully. I should read carefully…
Comment: Correlating DNA methylation beta values with Gene expression levels (RNA-seq)
by
Hamid Ghaedi
★ 2.5k
Oh I see, to make the code work, I modified the it a bit. So there is no need to make `tmp` data frame anymore also I added `as.numeric()` …
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