Latest
Open
Jobs
Tutorials
Tags
About
FAQ
Community
Planet
New Post
Log In
New Post
Latest
Open
News
Jobs
Tutorials
Forum
Tags
Planet
Users
Log In
Sign Up
About
Limit : today
all time
today
this week
this month
this year
50 results • Page
1 of 1
Sort: Rank
Rank
Views
Votes
Replies
1
vote
1
reply
53
views
Bulk and Single Cell RNA-seq online course
single_cell_RNA-seq
bulk_RNA-seq
online_course
updated 18 minutes ago by
swbarnes2
13k • written 5 hours ago by
ire
• 0
0
votes
1
reply
16
views
gene set enrichment analysis- by enrichGO
rna-seq
GO
enrichment
updated 19 minutes ago by
Istvan Albert
99k • written 48 minutes ago by
CL
• 0
0
votes
0
replies
8
views
GO categorization
Ontology
Gene
21 minutes ago by
m.habib
• 0
0
votes
0
replies
7
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
40 minutes ago by
luckyday1661
• 0
0
votes
0
replies
8
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
42 minutes ago by
Nicolas
• 0
0
votes
0
replies
19
views
Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic
bioinformatic
2 hours ago by
Giovana
• 0
0
votes
0
replies
29
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
2 hours ago by
Tracey
• 0
0
votes
6
replies
508
views
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 2 hours ago by
Rebecca
• 0 • written 18 days ago by
ellen.francis
• 0
0
votes
0
replies
33
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
2 hours ago by
Trevor
• 0
0
votes
0
replies
37
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
3 hours ago by
bioinfo
▴ 140
0
votes
1
reply
86
views
Where do these snpeff annotation come from?
snpeff
updated 3 hours ago by
Istvan Albert
99k • written 6 hours ago by
curious
▴ 730
1
vote
2
replies
86
views
Is there a need to batch correct FPKM or TPM values for within sample comparison
Batch
correction
updated 2 hours ago by
ATpoint
78k • written 5 hours ago by
CTLong
▴ 20
0
votes
0
replies
40
views
Should I scale all genes in single cell Seurat?
singlecell
4 hours ago by
synat.keam
▴ 80
3
votes
5
replies
802
views
Extracting only soft/hard clipped reads from a bam file
bam
reads
NGS
clipped
data_analysis
updated 4 hours ago by
Pierre Lindenbaum
158k • written 14 months ago by
jcn
▴ 30
0
votes
3
replies
148
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 4 hours ago by
Istvan Albert
99k • written 8 hours ago by
Jingfang
• 0
2
votes
2
replies
193
views
BBtools bug in reporting the number of substitutions in the console output, it seems to report insanely high rates of heterozygosity
SNP
bbtools
updated 2 hours ago by
harold.smith.tarheel
★ 4.9k • written 7 hours ago by
Axzd
▴ 50
0
votes
1
reply
50
views
News:
Course: Genome Assembly and Annotation
GenomeAssembly
GenomeAnnotation
Longreads
Bioinformatics
Biodiversity
updated 6 hours ago by
sil_bioinfo
▴ 30 • written 6 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
188
views
How I add new organism "Beauveria bassiana (strain ARSEF 2860)" in ClueGo plug-in of cytoscape?
cytoscape
updated 6 hours ago by
Scooter
▴ 180 • written 25 days ago by
A
• 0
0
votes
1
reply
224
views
Gene Ontology enrichment with BINGO and ClueGO
BINGO
Cytoscape
ClueGO
Gene
Ontology
updated 6 hours ago by
Scooter
▴ 180 • written 13 days ago by
David R
▴ 20
0
votes
1
reply
145
views
String App in Cytoscape
App
String
cytoscape
updated 6 hours ago by
Scooter
▴ 180 • written 2 days ago by
hellokwmin
• 0
2
votes
5
replies
252
views
Tools or R / Python packages to perfom ML models
Python
machine-learning
R
transcriptomics
updated 3 hours ago by
Michael
53k • written 9 hours ago by
sil_bioinfo
▴ 30
0
votes
1
reply
92
views
Salmon indices differences
salmon
RNAseq
index
refgenie
decoy
updated 9 hours ago by
ATpoint
78k • written 10 hours ago by
enee
▴ 10
3
votes
2
replies
229
views
Mapping quality in `vg giraffe`
vg
10 hours ago by
Wenhai
• 0
0
votes
1
reply
97
views
PAML Troubleshooting Help
PAML
codeml
updated 6 hours ago by
dthorbur
▴ 880 • written 11 hours ago by
sebabiokr
▴ 10
0
votes
4
replies
182
views
Can you help me to download list of miRNA from a SRA under a bioproject ?
bioproject
mirna
updated 8 hours ago by
ATpoint
78k • written 11 hours ago by
abourrieau
• 0
0
votes
0
replies
59
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
12 hours ago by
hellokwmin
• 0
2
votes
2
replies
159
views
R script in docker
R
Visual_studio_code
Docker
6 hours ago by
mrashad
▴ 70
1
vote
3
replies
151
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 9 hours ago by
Basti
★ 1.8k • written 13 hours ago by
CTLong
▴ 20
0
votes
0
replies
52
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
14 hours ago by
maxlaubstein
• 0
0
votes
3
replies
141
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
12 hours ago by
J
• 0
0
votes
3
replies
164
views
ERROR FILE EXTENSION
Prokka
15 hours ago by
syirah4
• 0
0
votes
1
reply
120
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
updated 15 hours ago by
Tao
▴ 30 • written 1 day ago by
Bryan
▴ 10
0
votes
9
replies
401
views
Where is the index command?
samtools
updated 9 hours ago by
Michael
53k • written 1 day ago by
luque007
• 0
0
votes
0
replies
78
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
23 hours ago by
luckyday1661
• 0
0
votes
2
replies
183
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 10 hours ago by
fracarb8
★ 1.3k • written 23 hours ago by
synat.keam
▴ 80
2
votes
2
replies
198
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 8 hours ago by
ATpoint
78k • written 1 day ago by
newbee
▴ 40
0
votes
1
reply
123
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 11 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
tss243
• 0
0
votes
0
replies
100
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
7 hours ago by
aheinzel
▴ 130
3
votes
3
replies
179
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 19 hours ago by
Jeremy
▴ 840 • written 1 day ago by
ohtang7
▴ 40
8
votes
7
replies
439
views
p-value combination methods
rnaseq
NB-GLM
p-value
meta-Analysis
updated 4 hours ago by
Istvan Albert
99k • written 2 days ago by
sehriban.buyukkilic
• 0
2
votes
3
replies
192
views
Blastn DB issue
cgmlst
blastn
updated 18 hours ago by
Philipp Bayer
8.1k • written 1 day ago by
hakhasan
• 0
1
vote
2
replies
188
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
14 hours ago by
eamaunders
• 0
0
votes
3
replies
254
views
Viral genes not showing up in combined mouse+virus alignment
RNAseq
22 hours ago by
cook.675
▴ 210
0
votes
5
replies
298
views
HTseq reports missing attribute name
htseq
updated 7 hours ago by
Istvan Albert
99k • written 3 days ago by
Bjorn
• 0
0
votes
1
reply
208
views
htShinyExample-5.3 - not working
htShiny
Oncoprint
InteractiveComplexHeatmap
updated 20 hours ago by
Ram
41k • written 6 days ago by
bioinfo
▴ 60
2
votes
9
replies
646
views
Salmon (or other pseudo-mappers) for multi-species RNAseq read filtering
STAR
Salmon
mapper
aligner
RNAseq
23 hours ago by
ian.will
▴ 10
8
votes
8
replies
552
views
How to filter .fasta file based on conditional statement
abundance
filtering
fasta
vsearch
updated 3 hours ago by
Brian Bushnell
19k • written 8 days ago by
rob_DNA
▴ 20
0
votes
2
replies
233
views
Can FPKM be used to create bar graphs for DEGs?
RNA-seq
3 hours ago by
junli1988
• 0
2
votes
11
replies
658
views
Data preparation for a ML model
machine-learning
RNA-Seq
R
python
biomarkers
5 hours ago by
sil_bioinfo
▴ 30
0
votes
2
replies
832
views
Ipyrad de novo for variant calling
snps
updated 2 hours ago by
Betsy
• 0 • written 2.5 years ago by
giulia.trauzzi
▴ 10
50 results • Page
1 of 1
Recent Votes
Answer: Bulk and Single Cell RNA-seq online course
Answer: Is there a need to batch correct FPKM or TPM values for within sample comparison
A: RNA-Seq post-DGE "Diagnostic tests"
Comment: p-value combination methods
Comment: p-value combination methods
Answer: Which Tools do you use for (Tandem) Repeat Detection? Why?
C: Run Makeblastdb For Compressed File
Recent Locations •
All
United States,
just now
Chile,
just now
Memphis, TN,
3 minutes ago
Ohio, USA,
5 minutes ago
United States,
6 minutes ago
United States,
7 minutes ago
United States,
7 minutes ago
Recent Awards •
All
Popular Question
to
Shicheng Guo
★ 9.3k
Popular Question
to
prasundutta87
▴ 660
Popular Question
to
massa.kassa.sc3na
▴ 590
Commentator
to
dsull
★ 5.1k
Scholar
to
Xian
▴ 60
Popular Question
to
sebabiokr
▴ 10
Popular Question
to
emmanouil.a
▴ 120
Recent Replies
Answer: Bulk and Single Cell RNA-seq online course
by
swbarnes2
13k
I'd start by getting tutorials for R libraries like DESeq, EdgeR, Seurat, etc, and learn by doing.
Answer: gene set enrichment analysis- by enrichGO
by
Istvan Albert
99k
Some analyses compare a subset of genes to a background. In those cases you would need to select a subset via some attributes like pvalues …
Comment: Ipyrad de novo for variant calling
by
Betsy
• 0
Were you ever able to resolve this error? I am having the exact same problem trying to run ipyrad on already demultiplexed fq.gz files
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
ATpoint
78k
Depends on the analysis. If you do some sort of gene ratio calculation then probably yes. Batch correction does not affect all genes equall…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
Rebecca
• 0
If there is a copy of the wgcna pdfs available please let me know!
Comment: How to filter .fasta file based on conditional statement
by
Brian Bushnell
19k
You're using BBTools v39.01. I just added the new flag in 39.06 :)
Answer: Where do these snpeff annotation come from?
by
Istvan Albert
99k
in principle you can do a snpeff dump hg38 that will generate a text output of the content of the database. in practice when I …
Comment: Can FPKM be used to create bar graphs for DEGs?
by
junli1988
• 0
LOL...It's a CSV file, and that's all I have in the folder. I agree that it is indeed the stuff of nightmares. But what can I do? It's not …
Answer: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
jv
★ 1.2k
My assumption is that intra-sample comparisons should not require batch effect correction.
Comment: Tools or R / Python packages to perfom ML models
by
Michael
53k
If you have a lot of training data with class labels, as your dataset seems to be you could turn it into an ML classification problem. Gene…
Comment: p-value combination methods
by
Istvan Albert
99k
https://www.biostars.org/u/41501/ please don't delete post that have additional content associated with them having assistance from the C…
Comment: In what case there are RR reads but no LL reads when detect inversions using IGV
by
Istvan Albert
99k
I think a view as pairs is much cleaner as it shows the actual pairing and how they cross the gap. In the view you show it is not clear whe…
Answer: Extracting only soft/hard clipped reads from a bam file
by
Pierre Lindenbaum
158k
only soft clipped reads (but should be ok in most cases, as in bwa only secondary reads are hard clipped): samtools view -O BAM -o ou…
Comment: In what case there are RR reads but no LL reads when detect inversions using IGV
by
Jingfang
• 0
Thanks for your reply. The IGV image I show used color alignments by pair orientation, and view mate region in split screen. Blue reads …
Answer: Extracting only soft/hard clipped reads from a bam file
by
horeyezonr
▴ 10
Hi I know it was more than a year, but I'll just leave the answer here maybe it will help someone. With the modified code of yours, th…
Traffic: 2102 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6