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1,000 results • Page
5 of 20
Sort: Rank
Rank
Views
Votes
Replies
1
vote
0
replies
148
views
DESeq2 comparing timepoints within treatment and account for background control change
RNAseq
DEG
DESeq2
updated 8 days ago by
Ram
43k • written 8 days ago by
ian.will
▴ 30
2
votes
0
replies
113
views
News:
Online Course Generalised Additive Mixed Models (GAMM): modelling space-time correlation structures
GAMM
Rlang
Rstats
Rproject
updated 8 days ago by
Ram
43k • written 8 days ago by
Transmitting Science communication
▴ 70
2
votes
0
replies
108
views
News:
Online Course Introduction to Network Analysis and Modelling
Python
Network-Analysis
updated 8 days ago by
Ram
43k • written 8 days ago by
Transmitting Science communication
▴ 70
1
vote
3
replies
267
views
Merging vcf files with bcftools ([E::get_intv] Failed to parse TBX_VCF, was wrong -p [type] used?)
vcf
tabix
bcftools
updated 2 days ago by
Pierre Lindenbaum
161k • written 8 days ago by
giulia.cosenza
• 0
0
votes
0
replies
101
views
Surrogate variable analysis for paired RNA seq experiment
sva
rnaseq
ruvseq
8 days ago by
nhaus
▴ 300
1
vote
3
replies
257
views
True variants selection
vcf
bcftools
updated 7 days ago by
dthorbur
★ 1.9k • written 8 days ago by
maevalefeuvre
• 0
0
votes
1
reply
150
views
How to reveal real AF of variant if duplicates can't be removed (such as in amplicon-seq)
allele-frequency
amplicon-seq
updated 8 days ago by
Ram
43k • written 8 days ago by
CY
▴ 750
0
votes
0
replies
97
views
Creating a BSgenome data package from a NCBI assembly - Virus
Virus
BSgenomeForge
BSgenome
R
8 days ago by
JirMan
▴ 20
2
votes
6
replies
429
views
KEGG analysis in R
KEGG
clusterProfiler
Zea-mays
8 days ago by
sansan_96
▴ 80
1
vote
1
reply
165
views
Failed to download data from EBI with ascp
EBI
aspera
updated 8 days ago by
GenoMax
141k • written 8 days ago by
biock
▴ 60
0
votes
0
replies
389
views
BETA whether on the same scale when performing rank-based inverse normal transformation on the same type of phenotype data for two cohorts separately…
normal
inverse
transformation
8 days ago by
Isaac
• 0
0
votes
0
replies
99
views
Combining VG graphs
vg
graphs
combine
8 days ago by
AshleeThomson
▴ 70
1
vote
3
replies
302
views
Why is DESeq2 normalization making my top feature have identical values across samples?
DESEQ2
WGCNA
8 days ago by
DNAngel
▴ 250
2
votes
2
replies
276
views
Creating a cytoscape bubble figure
cytoscape
network
GO
8 days ago by
Dave Carlson
★ 1.7k
3
votes
3
replies
320
views
Disrupting a gene interaction network
cytohubba
cytoscape
sequences
mRNA
8 days ago by
george
• 0
3
votes
1
reply
257
views
ClueGO is not showing custom data
ClueGo
Cytoscape
updated 8 days ago by
Scooter
▴ 280 • written 15 days ago by
Nicolas
• 0
2
votes
7
replies
5.1k
views
9 follow
problem with HOMER findMotifsGenome.pl
HOMER
ATAC-Seq
updated 8 days ago by
kaaz
• 0 • written 5.5 years ago by
ste.lu
▴ 80
5
votes
3
replies
303
views
Best genome browser for manual curation of gene structure(s)?
structure
gene
updated 7 days ago by
cmdcolin
★ 3.8k • written 9 days ago by
William
★ 5.3k
1
vote
7
replies
5.0k
views
How do I plot several sns.clustermap heatmaps in a single figure?
python
seaborn
updated 8 days ago by
Wubin
▴ 40 • written 3.4 years ago by
roy.granit
▴ 880
0
votes
1
reply
183
views
Human Methylation Infinum Bead - probe to gene mapping
TCGA
pancan
data
updated 8 days ago by
Zhenyu Zhang
★ 1.2k • written 9 days ago by
shrutidesai0208
• 0
1
vote
4
replies
364
views
Is it just me or has www.ensembl.org been broken for a while?
ensembl
8 days ago by
gene_biostars
• 0
0
votes
0
replies
102
views
Installing SALSA and HIRise scafolding software
scafolding
SALSA
genome-assembly
HIRise
updated 8 days ago by
Ram
43k • written 9 days ago by
Lissa Cruz Saavedra
• 0
0
votes
1
reply
174
views
Extract Di-nucleotide/Tri-Nucleotide substitution frequencies from MSA/VCF file
MSA
substitution
VCFstats
Evolution
VCF
updated 9 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
Saran
▴ 50
0
votes
2
replies
257
views
Abundance Calculation in MetaPhlAn 3: Methodology, TPM or RPKM, and the Treatment of Unclassified Reads
MetaPhlAn
Normalization
RPKM
TPM
6 days ago by
ramin.k2013
• 0
0
votes
0
replies
154
views
Normalization in Metagenomics Sequencing By Total Number of Reads: Pre- or Post-Filtering and the Role of Unclassified Reads
Normalization
Metagenomics
updated 8 days ago by
Ram
43k • written 9 days ago by
ramin.k2013
• 0
1
vote
2
replies
188
views
Finding variants within a subset of a BAM file
variant
calling
updated 9 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
ramiro.barrantes
• 0
0
votes
1
reply
162
views
convert h5ad to rds
single-cell
transcriptome
updated 9 days ago by
bk11
★ 2.3k • written 9 days ago by
lucas.aleixoleal17
• 0
1
vote
2
replies
210
views
Error during demultiplexing by bcl2fastq
bcl2fastq
updated 9 days ago by
GenoMax
141k • written 9 days ago by
daffodil
▴ 10
0
votes
1
reply
156
views
Help with generating annotation database for dog genome to use in ANNOVAR for variant annotation of dog tumor sequences
ANNOVAR
updated 9 days ago by
Pierre Lindenbaum
161k • written 9 days ago by
sainavyav22
• 0
0
votes
1
reply
501
views
Clair3 very low F1 INDEL score
ont
clair3
nanopore
wgs
updated 9 days ago by
yussab
▴ 90 • written 21 months ago by
Satrio
• 0
0
votes
9
replies
553
views
99.9999% of Q30 bases is normal?
RNA-seq
fastp
updated 7 days ago by
LauferVA
4.2k • written 9 days ago by
Aki
▴ 10
0
votes
0
replies
88
views
Issue while using circle_dat function from GOplot in R
GOplot
R
9 days ago by
ckelly96
• 0
1
vote
7
replies
403
views
fastp - can I trim specific adapters only?
trimming
fastp
adapter
8 days ago by
liorglic
★ 1.4k
0
votes
2
replies
176
views
Can't figure out plink --sample-diff
plink
9 days ago by
curious
▴ 750
0
votes
1
reply
5.0k
views
How to compute a one tail (one way) log rank test for survival?
R
survival
hypothesis-testing
log-rank
updated 8 days ago by
jack
• 0 • written 7.5 years ago by
denalitastic
▴ 30
0
votes
1
reply
136
views
Geneious Prime (Consense Sequence)
Consense
Sequence
updated 9 days ago by
GenoMax
141k • written 9 days ago by
Reno
• 0
0
votes
4
replies
226
views
Downsampling long-read BAM files
nanopore
BAM
QC
ONT
downsampling
updated 9 days ago by
GenoMax
141k • written 9 days ago by
eesiribloom
▴ 80
1
vote
2
replies
205
views
convert a seurat object to expressionset
Seurat
8 days ago by
Bine
▴ 60
2
votes
0
replies
105
views
News:
Course Functional Programming with R
Rstats
TScourses
Rproject
KeepLearning
Rlang
9 days ago by
Transmitting Science communication
▴ 70
1
vote
1
reply
159
views
Shared pathways up in disease blood and tissue relative to healthy blood (scRNA-seq)
scRNA-seq
updated 9 days ago by
ATpoint
81k • written 9 days ago by
Lucy
▴ 140
2
votes
4
replies
377
views
Per Base Sequence Content - continuous raise of G%
fastqc
updated 9 days ago by
GenoMax
141k • written 10 days ago by
pl.terzian
• 0
0
votes
0
replies
109
views
Inferring cell identity/genotype in single cells with missing information
cell
seurat
single
score
9 days ago by
txema.heredia
▴ 110
0
votes
2
replies
182
views
fmols for nanopore library loading
nanopore
sequencing
libraryprep
fmol
LSK114
updated 9 days ago by
GenoMax
141k • written 9 days ago by
njornet
▴ 20
0
votes
0
replies
93
views
cibersortx colnames
gema122
9 days ago by
gem1
• 0
10
votes
37
replies
12k
views
21 follow
Convert Gene IDs of Tomato Sol Database
tomato
gene
updated 9 days ago by
aziz.hammou
• 0 • written 8.8 years ago by
kevluv93
▴ 170
0
votes
2
replies
250
views
Beagle imputation
beagle
9 days ago by
mahlet.teka
• 0
12
votes
2
replies
423
views
News:
8th Berlin Summer School in NGS Data Analysis (June 10-14, 2024) - already half booked
Workshop
RNA-Seq
DNA-Seq
Illumina
9 days ago by
David Langenberger
11k
0
votes
2
replies
211
views
How to detect and visualize ORFs in bacterial genome?
statistics
visualization
ORFs
genome
7 days ago by
marongiu.luigi
▴ 710
5
votes
13
replies
9.1k
views
8 follow
biomaRt: Timeout on getBM().
r
biomart
ensembl
updated 8 days ago by
Mike Smith
★ 2.0k • written 2.8 years ago by
lincaijin1994
▴ 40
0
votes
8
replies
5.3k
views
8 follow
cellranger mkref failed
next-gen-sequencing
software-error
RNA-seq
updated 9 days ago by
EricYang
• 0 • written 4.7 years ago by
Dan
▴ 180
1,000 results • Page
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Recent Votes
what's the genomic location and name of gene responsible for orange and black patches in calico cats
Comment: featureCounts --primary tag counting uniquely mapped reads and excludes multi-ma
Answer: Duplicate marking, read names, and the SRA
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Comment: Installing/switching between versions of R/Rstudio/Bioconductor
Answer: Cellranger count error: Input FASTQ file ended prematurely
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Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Matthias Zepper
4.5k
It is not entirely off, but evidently also not correct. Melanin biosynthesis is a multistep process, that indeed prominently involves the…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
> so a single Rscript could utilise multiple environments and versions How is that sane, let alone "better"? Also, why use `snap` for curl…
Comment: how to find genes that are significantly expressed in brain cortex samples
by
Ram
43k
Normalized how?
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
With public data one has to work with what is there. If the information about position is absent then only thing that could be done is to l…
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Or better yet. To have an R package that allows access to conda environments via "conda list env" so that environments can be switched with…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
If GPT is right then it says that: > The specific gene responsible for the orange and non-orange (black or > gray) fur colors in cats is t…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
Jean-Karim Heriche
27k
As far as I know the Orange locus hasn't been mapped to a gene. Maybe this paper will help in narrowing the search: https://www.ncbi.nlm.ni…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>Curios if there a reference for this? [Apparently it's not deprecated yet][1], but will be soon and the SRA intends for it to be at some …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
I prefer RStudio for new projects as well. The moment I need versions though, RStudio becomes a burden. I wish one could launch RStudio fro…
Comment: what's the genomic location and name of gene responsible for orange and black pa
by
GenoMax
141k
According to ChatGPT: The gene responsible for the orange and black patches of fur in calico cats (and tortoiseshell cats) is the X-linked …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
BioinfGuru
★ 1.7k
Certainly true. Switching versions is way simpler that way, at the cost of the familiarity of the Rstudio IDE - especially if the code is w…
Comment: Duplicate marking, read names, and the SRA
by
GenoMax
141k
> fastq-dump is deprecated Curios if there a reference for this? `fasterq-dump` seems to allow for parallel streams but `fastq-dump` is st…
Comment: Duplicate marking, read names, and the SRA
by
Luka
• 0
>In many cases those remain recoverable using the -F option when you dump the data (cloud download not required) The -F option (or any equ…
Answer: Duplicate marking, read names, and the SRA
by
GenoMax
141k
To be specific, not every dataset in SRA loses the original identifiers. In many cases those remain recoverable using the `-F` option when …
Comment: Installing/switching between versions of R/Rstudio/Bioconductor on personal mach
by
Ram
43k
To use different versions of R and bioconductor, you don't really need RStudio. One can simply create new conda environments with the requi…
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