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113,869 results • Page
1 of 2278
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0
votes
0
replies
11
views
DIAMOND tutorial
tutorial
DIAMOND
1 hour ago by
sooni
▴ 10
0
votes
13
replies
838
views
Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cell Ranger.
fixed-RNA-profiling
chromium
cellranger
scFFPE
updated 1 hour ago by
MohammadAlkadi
▴ 70 • written 5 weeks ago by
bk11
★ 1.8k
0
votes
2
replies
111
views
Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
metabolomic
bioinformatic
updated 2 hours ago by
Kevin Blighe
86k • written 8 hours ago by
Giovana
• 0
2
votes
8
replies
592
views
6 follow
WGCNA tutorial docs needed: Horvath Lab site down
WGCNA
updated 3 hours ago by
ATpoint
78k • written 18 days ago by
ellen.francis
▴ 10
0
votes
0
replies
43
views
How to estimate -g genome-size for Flye for de novo genome or for --meta mode when using Metaflye?
assembly
fasta
genomics
nanopore
pacbio
4 hours ago by
O.rka
▴ 710
0
votes
1
reply
326
views
Loftee no splice site annotations
Loftee
VEP
updated 5 hours ago by
AMARU
• 0 • written 21 months ago by
Filago
▴ 90
1
vote
1
reply
92
views
Bulk and Single Cell RNA-seq online course
single_cell_RNA-seq
bulk_RNA-seq
online_course
updated 5 hours ago by
swbarnes2
13k • written 10 hours ago by
ire
• 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
0
votes
1
reply
63
views
gene set enrichment analysis- by enrichGO
rna-seq
GO
enrichment
updated 5 hours ago by
Istvan Albert
99k • written 6 hours ago by
CL
• 0
0
votes
0
replies
41
views
GO categorization
Ontology
Gene
6 hours ago by
m.habib
• 0
0
votes
0
replies
33
views
how to download the VCF/MAF files from cBioportal genie site
cBioportal
mutation
VCF
TMB
6 hours ago by
luckyday1661
• 0
0
votes
0
replies
37
views
How to get multiple protein domain database domain name from id's
annotations
blast2go
domain
domains
proteins
6 hours ago by
Nicolas
• 0
0
votes
0
replies
51
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
4 hours ago by
Ty
• 0
0
votes
0
replies
45
views
Annotate Unplaced Scaffold with Chromosome Information
assembly
annotation
scaffold
Chromosome
8 hours ago by
Trevor
• 0
0
votes
0
replies
49
views
How to do KEGG pathway analysis when I have a gene with multiple entrez IDs?
biomart
kegg
deseq2
8 hours ago by
bioinfo
▴ 140
0
votes
1
reply
99
views
Where do these snpeff annotation come from?
snpeff
updated 8 hours ago by
Istvan Albert
99k • written 12 hours ago by
curious
▴ 730
3
votes
4
replies
149
views
Is there a need to batch correct FPKM or TPM values for within sample comparison
Batch
correction
51 minutes ago by
CTLong
▴ 20
0
votes
0
replies
48
views
Should I scale all genes in single cell Seurat?
singlecell
10 hours ago by
synat.keam
▴ 80
4
votes
5
replies
825
views
Extracting only soft/hard clipped reads from a bam file
bam
reads
NGS
clipped
data_analysis
updated 10 hours ago by
Pierre Lindenbaum
158k • written 14 months ago by
jcn
▴ 30
0
votes
3
replies
166
views
In what case there are RR reads but no LL reads when detect inversions using IGV?
IGV
inversion
updated 10 hours ago by
Istvan Albert
99k • written 14 hours ago by
Jingfang
• 0
3
votes
2
replies
252
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 7 hours ago by
harold.smith.tarheel
★ 4.9k • written 12 hours ago by
Axzd
▴ 50
0
votes
1
reply
63
views
News:
Course: Genome Assembly and Annotation
GenomeAssembly
GenomeAnnotation
Longreads
Bioinformatics
Biodiversity
updated 11 hours ago by
sil_bioinfo
▴ 30 • written 11 hours ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
195
views
How I add new organism "Beauveria bassiana (strain ARSEF 2860)" in ClueGo plug-in of cytoscape?
cytoscape
updated 12 hours ago by
Scooter
▴ 180 • written 25 days ago by
A
• 0
0
votes
1
reply
234
views
Gene Ontology enrichment with BINGO and ClueGO
BINGO
Cytoscape
ClueGO
Gene
Ontology
updated 12 hours ago by
Scooter
▴ 180 • written 13 days ago by
David R
▴ 20
0
votes
1
reply
153
views
String App in Cytoscape
App
String
cytoscape
updated 12 hours ago by
Scooter
▴ 180 • written 3 days ago by
hellokwmin
• 0
2
votes
5
replies
273
views
Tools or R / Python packages to perfom ML models
Python
machine-learning
R
transcriptomics
updated 9 hours ago by
Michael
53k • written 15 hours ago by
sil_bioinfo
▴ 30
0
votes
1
reply
100
views
Salmon indices differences
salmon
RNAseq
index
refgenie
decoy
updated 15 hours ago by
ATpoint
78k • written 16 hours ago by
enee
▴ 10
3
votes
2
replies
238
views
Mapping quality in `vg giraffe`
vg
16 hours ago by
Wenhai
• 0
0
votes
1
reply
108
views
PAML Troubleshooting Help
PAML
codeml
updated 12 hours ago by
dthorbur
▴ 880 • written 17 hours ago by
sebabiokr
▴ 10
0
votes
4
replies
192
views
Can you help me to download list of miRNA from a SRA under a bioproject ?
bioproject
mirna
updated 16 hours ago by
Nitin Narwade
★ 1.5k • written 17 hours ago by
abourrieau
• 0
0
votes
0
replies
66
views
how to calculate intramodular connectivity
WGCNA
intramodularConnectivity
18 hours ago by
hellokwmin
• 0
2
votes
2
replies
168
views
R script in docker
R
Visual_studio_code
Docker
12 hours ago by
mrashad
▴ 70
2
votes
3
replies
164
views
Is bisulfite-seq data from different studies comparable with each other?
Methylation
updated 15 hours ago by
Basti
★ 1.9k • written 19 hours ago by
CTLong
▴ 20
0
votes
0
replies
58
views
ADMIXTURE Freezes Right Before Completion
ADMIXTURE
admixture
19 hours ago by
maxlaubstein
• 0
0
votes
3
replies
149
views
calculate nucleotide diversity from whole-genome-sequence data for individual genes
genomics
nucleotide_diversity
vcf
18 hours ago by
J
• 0
0
votes
3
replies
172
views
ERROR FILE EXTENSION
Prokka
20 hours ago by
syirah4
• 0
0
votes
1
reply
126
views
filtering SAM/BAM to remove hits spanning short combined alignment lengths and low counts
align
bbmap
metagenomics
updated 21 hours ago by
Tao
▴ 30 • written 1 day ago by
Bryan
▴ 10
0
votes
9
replies
419
views
Where is the index command?
samtools
updated 15 hours ago by
Michael
53k • written 1 day ago by
luque007
• 0
0
votes
0
replies
90
views
GATK Mutect2 mouse dbSNP vcf files recommendations for mouse whole exome data
mouse
GATK
Mutect2
dbSNP
1 day ago by
luckyday1661
• 0
0
votes
2
replies
193
views
Cellcyclescoring did not work in Seurat V5
singlecell
updated 16 hours ago by
fracarb8
★ 1.3k • written 1 day ago by
synat.keam
▴ 80
0
votes
0
replies
78
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
1 day ago by
DINESHR
• 0
2
votes
2
replies
207
views
scRNA-seq: Consistent low number of cells and low fraction reads across the samples
scRNA-seq
cells
mRNA
expression
gene
updated 14 hours ago by
ATpoint
78k • written 1 day ago by
newbee
▴ 40
0
votes
0
replies
94
views
deeptools k-means clustering
heatmap
deeptools
chipseq
1 day ago by
biology_inform
▴ 50
0
votes
1
reply
129
views
How to check for incorporation of plasmid DNA into human genomic DNA (ChIP-seq)?
plasmid
chipseq
updated 16 hours ago by
Nitin Narwade
★ 1.5k • written 1 day ago by
tss243
• 0
3
votes
6
replies
355
views
Generate Read counts from bam file
RNAseq
reference_genome
Deseq2
read_counts
updated 1 day ago by
NextGenSeek
• 0 • written 2 days ago by
singhankit973
• 0
0
votes
2
replies
175
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 1 day ago by
GenoMax
136k • written 1 day ago by
JACKY
▴ 120
0
votes
0
replies
110
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
13 hours ago by
aheinzel
▴ 130
3
votes
3
replies
192
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 1 day ago by
Jeremy
▴ 840 • written 1 day ago by
ohtang7
▴ 40
0
votes
0
replies
85
views
Conumee output as input for Gistic2.0
cnv
copy
gistic
cna
conumee
updated 1 day ago by
GenoMax
136k • written 1 day ago by
sativus
▴ 10
0
votes
0
replies
100
views
Population study based on metaT and MetaG
metagenome
metatranscriptome
study
population
updated 1 day ago by
GenoMax
136k • written 1 day ago by
PierreGT
• 0
113,869 results • Page
1 of 2278
Recent Votes
C: Extract soft-clipped reads from BWA -generated SAM file
Comment: Is bisulfite-seq data from different studies comparable with each other?
Answer: Is there a need to batch correct FPKM or TPM values for within sample comparison
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
A: what do the headers of the rMATS output files mean?
A: what do the headers of the rMATS output files mean?
Answer: BBtools bug in reporting the number of substitutions in the console output, it s
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Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's what I would assume, because we are not taking into account cross sample differences here. Thanks
Comment: Is there a need to batch correct FPKM or TPM values for within sample comparison
by
CTLong
▴ 20
That's a good point. So its probably safest to not batch correct for within sample comparisons I guess?
Answer: Generating count matrix from Chromium Fixed RNA Profiling (FRP) data outside Cel
by
MohammadAlkadi
▴ 70
What is the purpose of doing so? I tried to do that by using the bam file generated by CellRanger. One **important detail** if you are work…
Comment: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Thank you - appreciate the translation.
Answer: Guidance on Crucial Parameters for Bioinformatic Analysis of Metabolomic Data
by
Kevin Blighe
86k
Em geral, uma taxa de descoberta falsa de 5% (p ajustado<0,05 ) deve ser usada para qualquer teste estatístico em que múltiplas hipóteses i…
Answer: WGCNA tutorial docs needed: Horvath Lab site down
by
ATpoint
78k
See link here from the developer: https://bioinformatics.stackexchange.com/a/21886/16676
Comment: WGCNA tutorial docs needed: Horvath Lab site down
by
Katie
• 0
I would also appreciate the PDFs if anyone has them please
Answer: Loftee no splice site annotations
by
AMARU
• 0
Hey, did you solve it? I am having a very similar issue. Thanks
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…
Comment: 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 …
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