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176 results • Page
3 of 4
Sort: replies
Rank
Views
Votes
Replies
1
vote
2
replies
302
views
Merging several vcf files for GWAS?
R
beginner
gwas
ngs
novogene
5 days ago by
sabrilo171
• 0
1
vote
2
replies
173
views
RnBeads which p-value to use
Methylation
RnBeads
updated 2 days ago by
ATpoint
78k • written 2 days ago by
a.basitkhan1990
▴ 30
0
votes
2
replies
49
views
How can I adjust Y-axis scale when making relative abundance box plot ?
statistics
box-plot
R
scale_adjustment
logarithm
updated 2 hours ago by
ATpoint
78k • written 2 hours ago by
ohtang7
▴ 30
1
vote
2
replies
142
views
Problem in installing 'magick' R package
R
installation
package
magick
updated 9 hours ago by
DBScan
▴ 210 • written 12 hours ago by
applepie
• 0
0
votes
2
replies
40
views
What type of cancer did they study in this paper?
cancer
RNAseq
single-cell
updated 1 hour ago by
GenoMax
136k • written 1 hour ago by
JACKY
▴ 120
0
votes
2
replies
255
views
Creating a Variant containing FASTA for proteomics search from VCF and genomic FASTA
translation
Variant
proteomics
FASTA
VCF
6 days ago by
chscho
• 0
3
votes
2
replies
153
views
Moving AF tag to new column in a VCF file
mutect2
vcf
20 hours ago by
Christian
▴ 30
0
votes
2
replies
1.4k
views
AttributeError: module 'collections' has no attribute 'Hashable'
Spades
updated 11 hours ago by
jiyoung
▴ 20 • written 7 months ago by
Hayler Edu
▴ 30
1
vote
2
replies
192
views
DOES MGI SEQUENCING RESULT CONTAINS MULTIPLE FILES FOR SINGLE SAMPLE
whole
genome
assembly
sequencing
updated 6 days ago by
WouterDeCoster
47k • written 6 days ago by
manaswiniparija3
▴ 10
0
votes
2
replies
169
views
Comparing 3 Data Sets using DeSeq and Heatmaps
DeSeq
Normalization
21 hours ago by
harter-ainsworth.izaak
• 0
0
votes
2
replies
681
views
CPAT: error on coding probability cutoff
lncRNA
RNAseq
CPAT
updated 2 days ago by
catarinaventura_pt
• 0 • written 21 months ago by
xiaoxia8923
• 0
0
votes
2
replies
183
views
RnBeads mean difference vs M-values
Methylation
updated 2 days ago by
Basti
★ 1.8k • written 2 days ago by
a.basitkhan1990
▴ 30
1
vote
1
reply
152
views
How should I run ssgsea analysis ?
functional
TPM
enrichment
gsea
ssgsea
updated 21 hours ago by
singh.vijender
▴ 100 • written 1 day ago by
DareDevil
★ 3.3k
2
votes
1
reply
172
views
What is Bowtie2 --norc parameter?
bowtie2
norc
alignment
updated 6 days ago by
ATpoint
78k • written 6 days ago by
lvl2111
• 0
1
vote
1
reply
291
views
After merging batches, I got very segmented umap in scanpy
scanpy
single-cell
5 days ago by
MohammadAlkadi
▴ 70
1
vote
1
reply
208
views
Genetic data QC prior to imputation
imputation
updated 5 days ago by
Raony Guimarães
★ 1.3k • written 5 days ago by
kl
▴ 10
0
votes
1
reply
236
views
MinKNOW software installation doubt for MinION Nanopore sequencing
MinKNOW
MinION
Nanopore
updated 4 days ago by
GenoMax
136k • written 5 days ago by
Soumajit
▴ 40
0
votes
1
reply
236
views
issue in RNA -seq analysis
NGS
RNA-Seq
updated 4 days ago by
GenoMax
136k • written 4 days ago by
subhiksha
• 0
1
vote
1
reply
253
views
Forum:
want to work in open source project/project in bioinformatics
bioinformatics
project
updated 3 days ago by
Matthias Zepper
4.2k • written 4 days ago by
Afeef
• 0
1
vote
1
reply
516
views
fragments.tsv.gz file in ATAC seq
ATAC-seq
updated 2 days ago by
tingting
▴ 10 • written 7 months ago by
Chris
▴ 230
1
vote
1
reply
150
views
Beginner differential methylation analysis
Methylation
updated 2 days ago by
Basti
★ 1.8k • written 2 days ago by
a.basitkhan1990
▴ 30
2
votes
1
reply
146
views
Bedtools intersection
bedtools
bed
intersect
vcf
updated 2 days ago by
Pierre Lindenbaum
158k • written 2 days ago by
rejoeraymond776
▴ 10
0
votes
1
reply
173
views
multiple condition and time course in RNA-seq
edgeR
RNA-Seq
DESeq2
updated 2 days ago by
i.sudbery
18k • written 3 days ago by
tiancaigg
▴ 30
1
vote
1
reply
173
views
Choose between pvalue & pvalue.adj
volcanoplot
updated 2 days ago by
Istvan Albert
99k • written 2 days ago by
Guitout
• 0
0
votes
1
reply
151
views
Combine Geoids
Geoids
NCBI
updated 2 days ago by
ATpoint
78k • written 2 days ago by
anasjamshed
▴ 120
0
votes
1
reply
185
views
Chipseq peak calling and peak frequency region
chipseeker
macs2
updated 1 day ago by
Arup Ghosh
3.2k • written 3 days ago by
Mehwish
▴ 10
0
votes
1
reply
241
views
Diferences between TCGAbiolinks and cBioportal
R
TCGAbiolinks
cBioportal
updated 1 day ago by
Zhenyu Zhang
★ 1.1k • written 6 days ago by
jomagrax
▴ 40
1
vote
1
reply
144
views
Mapping quality in `vg giraffe`
vg
updated 1 day ago by
Xian
▴ 40 • written 1 day ago by
Wenhai
• 0
0
votes
1
reply
128
views
Python function to export the annotated records to genbank file using python and biopython
biopython
python
bioinformatic
programming
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
Saurabh
• 0
2
votes
1
reply
136
views
unicycler error : [Errno 13] Permission denied:
unicycler
updated 1 day ago by
barslmn
★ 2.0k • written 1 day ago by
jiyoung
▴ 20
0
votes
1
reply
130
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
2
votes
1
reply
225
views
EnhancedVolcano underrepresenting DEGs
R
updated 1 day ago by
Kevin Blighe
86k • written 3 days ago by
jabbari.parnian
▴ 30
0
votes
1
reply
106
views
VCF conservation into Treemix
Treemix
Plink
VCF
updated 22 hours ago by
singh.vijender
▴ 100 • written 23 hours ago by
reza
▴ 300
2
votes
1
reply
203
views
Shorten Illumina reads
RepeatExplorer2
Illumina
paired-end
updated 6 days ago by
Brian Bushnell
19k • written 7 days ago by
kirillkirilenko
▴ 20
0
votes
1
reply
110
views
bam or VCF files from GSE75010
bam
file
or
VCF
updated 20 hours ago by
ATpoint
78k • written 21 hours ago by
ahonya
• 0
0
votes
1
reply
301
views
FVA on Sybil
R
Sybil
metabolic
fba
fva
updated 9 hours ago by
Thomas
• 0 • written 22 months ago by
isM15
• 0
0
votes
1
reply
144
views
Harmony integration PC variance explained
scRNA
integration
harmony
updated 6 hours ago by
CTLong
▴ 10 • written 2 days ago by
e.iich
• 0
0
votes
1
reply
112
views
How to create a mutation frequency comparison plot?
R
data-visualization
plot
updated 5 hours ago by
rpolicastro
12k • written 13 hours ago by
saipra003
▴ 10
0
votes
1
reply
96
views
How can I amend the output of a DIAMOND python script?
Python
Diamond
COG_analysis
updated 5 hours ago by
Nitin Narwade
★ 1.5k • written 7 hours ago by
eamaunders
• 0
1
vote
1
reply
126
views
How to get unaligned reads and aligned reads into separate files from SAM/BAM?
bam
sam
reads
fastq
updated 4 hours ago by
rpolicastro
12k • written 17 hours ago by
O.rka
▴ 710
1
vote
1
reply
89
views
Two identical reads in my bam files but with a different in CIGAR are mapped in a different location in IGV
pysam
4 hours ago by
ManuelDB
▴ 80
0
votes
1
reply
320
views
How to use conumee segment mean for gistic input
genomics
gistic
NGS
methylation
conumee
updated 3 hours ago by
sativus
▴ 10 • written 14 months ago by
Thind amarinder
▴ 340
1
vote
1
reply
149
views
Match variants for allele frequency, LD score, and other features
snp
2 hours ago by
Jautis
▴ 520
1
vote
0
replies
90
views
Visualize and explore eventalign data against reference
igv
minimap
nanopolish
nanopore
ngs
1 day ago by
joe
▴ 390
3
votes
0
replies
137
views
Herald:
The Biostar Herald for Monday, November 27, 2023
herald
2 days ago by
Biostar
2.3k
0
votes
0
replies
87
views
Differentiate sequenced and imputed variants in BGEN files
imputation
bgen
ukb
2 days ago by
user230613
▴ 350
0
votes
0
replies
19
views
Job:
Bioinformatican/Data Scientist, Transplant Immunology/Genetics, Medical University of Vienna, Austria
RiskPrediction
NGS
SNP
ExomeSequencing
GeneticRiskScore
1 hour ago by
aheinzel
▴ 130
0
votes
0
replies
95
views
addPatternDensity to qsea object
maxDensityPattern
medip
qsea
2 days ago by
Jaykishan
• 0
0
votes
0
replies
104
views
[maftools]Too many multi_hit and missense mutation
maftools
gatk
MAF
data
WES
VCF
3 days ago by
jiazheng_lin
• 0
0
votes
0
replies
117
views
Negative F statistics for sex check in plink
plink
check
sex
3 days ago by
kl
▴ 10
176 results • Page
3 of 4
Recent Votes
Answer: Generate Read counts from bam file
Comment: Generate Read counts from bam file
C: Heatmap : why scaling ?
Answer: How do I download a list of genes involved in cellular metabolism (in humans) ba
A: Incomplete reactome.org all pathway level to ENSEMBL ID annotation files
Comment: p-value combination methods
Comment: p-value combination methods
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Recent Replies
Comment: Best practices for differential expression analysis with low-yield Nanopore/ONT
by
tw_140
• 0
Thank you, I really appreciate your insight! I will look into the dropouts I have.
Answer: Generate Read counts from bam file
by
NextGenSeek
• 0
Are you analysing RNA or DNA heteroplasmy levels?
Comment: What type of cancer did they study in this paper?
by
GenoMax
136k
Perhaps the exact cancer type is not what is important. Looks like they are [**all solid tumors**][1] with a baseline sample and one after …
Comment: p-value combination methods
by
i.sudbery
18k
edgeR *is* an NB-GLM. The input to NB-GLMs, including edgeR and DESeq is read counts from each sample.
Answer: What type of cancer did they study in this paper?
by
jared.andrews07
★ 16k
Cutaneous or ocular melanoma. It's from [this paper](https://aacrjournals.org/cancerimmunolres/article/10/2/162/678013/NKG7-Is-a-T-cell-Int…
Comment: p-value combination methods
by
sehriban.buyukkilic
• 0
its output of edgeR. I'm asking for input of NB-GLM? what should be input of it?
Comment: How do I download a list of genes involved in cellular metabolism (in humans) ba
by
el24
▴ 40
Hi @pratik, Thanks for the helpful solution above. I'm working on a similar task in Mouse species and noticed the CTD database is human-spe…
Comment: Match variants for allele frequency, LD score, and other features
by
Jautis
▴ 520
Trying to bump this
Comment: p-value combination methods
by
i.sudbery
18k
The parameters you have here are the *output* of an NB-GLM, not the input to an NB-GLM (most likely edgeR?)
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
ATpoint
78k
Please provide data as dput(), not via any random dropbox, that could be anything (also malware, theoretically). If log transformation crea…
Comment: Extracting chimeric reads from mapping
by
doggie
• 0
Hi Pierre, so does samjdk support single-end reads for extracting chimeric reads? I've aligned my virus to the human reference, sorted the …
Comment: How can I adjust Y-axis scale when making relative abundance box plot ?
by
dthorbur
▴ 870
You can try `scale_y_sqrt()` instead if you don't like the look of the log10 transformation. As an aside, it doesn't look like your fill va…
Comment: Making multiple box plots with relative abundance in R
by
ohtang7
▴ 30
Thank you!! I really appreciate your help.
Comment: Making multiple box plots with relative abundance in R
by
rpolicastro
12k
In `scale_fill_manual` you have e.g. `"stray"` but in your data it's `"Stray"`. Just make sure the cases match.
Comment: How to use conumee segment mean for gistic input
by
sativus
▴ 10
Did you manage to find an answer to this question, i have done so myself, but would like to confirm that this methodology is sound?
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