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1,000 results • Page
1 of 20
Sort: Rank
Rank
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Votes
Replies
0
votes
0
replies
4
views
normalize for sample size in single cell rna seq cluster frequencies data
scRNAseq
seurat
10x
10 minutes ago by
chi.delta
▴ 40
0
votes
1
reply
15
views
snps from empty well, Illumina Sequencing
Illumina
SNP
sequencing
updated 27 minutes ago by
GenoMax
130k • written 34 minutes ago by
saint-even
• 0
0
votes
0
replies
10
views
TCGA input files for COHCAP
TCGA
methylation
COHCAP
1 hour ago by
dilrajkaur766
• 0
0
votes
0
replies
17
views
m6A-seq input normalisation with RNA-seq
m6A-seq
MeRIP-Seq
normalisation
deepTools
updated 1 hour ago by
Ram
39k • written 1 hour ago by
Pari
• 0
0
votes
1
reply
26
views
Is the Kruskal-Wallis test appropriate for genomic distances?
Statistics
Bioinformatics
updated 41 minutes ago by
ATpoint
72k • written 1 hour ago by
aaronlogsdon2001
• 0
0
votes
0
replies
22
views
Methylation (Illumina arrays or Whole-genome bisulfite sequencing WBS) and WGS datasets?
array
wgs
methylation
wbs
dna
2 hours ago by
cate.cevallos
• 0
1
vote
4
replies
88
views
How to use R installed by conda instead of it installed by apt on Ubuntu
R
ubuntu
conda
updated 36 minutes ago by
ATpoint
72k • written 2 hours ago by
Zhichao
• 0
0
votes
1
reply
44
views
Alternative To interactions comparison in limma in DESeq2
DESeq2
interactions
updated 2 hours ago by
ATpoint
72k • written 3 hours ago by
f2ff7a46
• 0
0
votes
1
reply
52
views
DESeq2 for different design and normalized counts
DESeq2
log2foldchange
updated 2 hours ago by
ATpoint
72k • written 3 hours ago by
t.ru
▴ 20
0
votes
1
reply
39
views
Visualizing several genomes/plasmids in a single figure
visualization
updated 1 hour ago by
GenoMax
130k • written 3 hours ago by
blur
▴ 270
1
vote
1
reply
49
views
switching from illumination to NEB prep kits
NEB
WGS
WES
illumina
updated 2 hours ago by
GenoMax
130k • written 3 hours ago by
lait
▴ 170
0
votes
0
replies
24
views
ERROR: LoadError: UndefVarError: `composition` not defined ?
Protpram
3 hours ago by
Sapphire
• 0
0
votes
0
replies
39
views
Complex Phylogenetic Tree Annotation
annotation
protein
phylogenetic-tree
updated 1 hour ago by
Ram
39k • written 4 hours ago by
Aanushka
• 0
0
votes
2
replies
1.6k
views
How to handle NaN in emmax Kinship matrix?
GWAS
SNP
updated 4 hours ago by
Thu
• 0 • written 5.1 years ago by
CWesse
• 0
1
vote
3
replies
115
views
Masking before RNA-Seq Alignment and Gene Prediction in Plant Genomes
RNA-evidence
genome
prediction
masking
updated 2 hours ago by
Darked89
4.4k • written 5 hours ago by
Ayish
• 0
0
votes
1
reply
76
views
What is the possibility of Depth (DP) being higher than the coverage
GATK
DP
Coverage
Depth
HaplotypeCaller
updated 9 hours ago by
seidel
11k • written 9 hours ago by
dare_devil
★ 3.1k
0
votes
2
replies
146
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
5 hours ago by
JACKY
▴ 100
0
votes
1
reply
109
views
CIBERSORT Error: File not found
CIBERSORT
updated 7 hours ago by
ATpoint
72k • written 17 hours ago by
jcara514
• 0
3
votes
4
replies
205
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 1 hour ago by
Ram
39k • written 19 hours ago by
shamza
• 0
0
votes
3
replies
224
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 16 hours ago by
Ram
39k • written 22 hours ago by
Researcher
• 0
1
vote
0
replies
99
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
1 day ago by
zhangdengwei
▴ 190
1
vote
2
replies
145
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
1 hour ago by
tahsinkhan570
• 0
2
votes
3
replies
218
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 1 day ago by
GenoMax
130k • written 1 day ago by
ev97
• 0
0
votes
0
replies
109
views
Which is the minor allele in ped file in plink?
plink
updated 1 day ago by
GenoMax
130k • written 1 day ago by
khn
▴ 130
0
votes
2
replies
189
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
16 hours ago by
mattze731
▴ 10
0
votes
0
replies
105
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
1 day ago by
F.Bedjou
▴ 10
0
votes
0
replies
87
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
1 day ago by
hashim.rana11
▴ 20
0
votes
0
replies
115
views
Integrate RDS files
integration
1 day ago by
Andy
▴ 50
0
votes
1
reply
162
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 6 hours ago by
ATpoint
72k • written 1 day ago by
akainth
▴ 10
1
vote
9
replies
321
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 1 day ago by
Ram
39k • written 1 day ago by
peavy
• 0
0
votes
1
reply
381
views
How to quantification proteomics data
proteomics
updated 1 day ago by
eqoa45
• 0 • written 19 months ago by
LeeLee
▴ 10
1
vote
4
replies
225
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
1 day ago by
Daniel
▴ 30
0
votes
2
replies
1.4k
views
How to perform statistical analysis of label free experiment using results from Proteome Discoverer?
Proteome-Discoverer
Label-Free
Proteomics
updated 1 day ago by
Ram
39k • written 4.5 years ago by
k2bhide
▴ 80
0
votes
0
replies
103
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
1 day ago by
eqoa45
• 0
1
vote
0
replies
112
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
1 day ago by
Dan
▴ 120
1
vote
2
replies
178
views
hisat2 Error 137
hisat2
RNA-seq
1 day ago by
Forough
▴ 10
0
votes
0
replies
110
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
2 days ago by
xeod21
• 0
2
votes
6
replies
298
views
Embryo transcriptome
database
transcriptome
SRA
updated 23 minutes ago by
Basti
★ 1.6k • written 2 days ago by
firefox91
• 0
1
vote
3
replies
182
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
2 days ago by
UserA
• 0
0
votes
0
replies
87
views
How to extract only neutral markers from low-coverage whole genome sequencing?
low-coverage
whole-genome-sequencing
updated 1 day ago by
Ram
39k • written 2 days ago by
beausoleilmo
▴ 530
0
votes
4
replies
202
views
Difference between USCS exon coordinates and ensembl
exons
Ensembl
1 day ago by
amy__
▴ 50
0
votes
0
replies
88
views
Why sone miRNAs are not present in TCGA data
TCGA
miRNA
RNA-seq
2 days ago by
nicolo.gualandi
• 0
0
votes
0
replies
78
views
Prediction of altrered metabolites from altered gene expression
Gene
Metabolites
2 days ago by
english.server
▴ 290
0
votes
6
replies
333
views
variant allelic fraction
vep
updated 23 hours ago by
Ram
39k • written 2 days ago by
Jom
• 0
0
votes
1
reply
146
views
Pairwise Alignment
Pairwise-Alignment
updated 1 day ago by
Ram
39k • written 2 days ago by
Fatemeh
• 0
0
votes
0
replies
95
views
How to perform a phylogenetic analysis from a vcf file
variants
haplotyping
phylogeny
vcf
3 days ago by
rj.rezwan
• 0
0
votes
1
reply
159
views
Where to get the molecular subtype information of STAD sample in TCGA
TCGA
database
updated 2 days ago by
Hamid Ghaedi
2.9k • written 3 days ago by
younglin113
▴ 50
0
votes
0
replies
136
views
How to keep ComplexHeatmap from reordering annotations
Dendrogram
HeatmapAnnotations
R
Heatmap
ComplexHeatmap
3 days ago by
Manuel
• 0
1
vote
3
replies
223
views
Differential protein expression analysis
R
proteomic
statistics
updated 3 hours ago by
dsull
★ 4.2k • written 3 days ago by
Ribo
▴ 40
0
votes
3
replies
322
views
(ERR): "index/Trinity.fa" does not exist or is not a Bowtie 2 index Exiting now ...
bowtie2
align_stats
trinity
2 days ago by
eimanpharmacist
▴ 20
1,000 results • Page
1 of 20
Recent Votes
Comment: ChatGPT optimized for bioinformatics questions
Answer: counts matrix should be numeric, currently it has mode: character when using a c
ChatGPT optimized for bioinformatics questions
Answer: Limma returned only positive logFC values
Answer: Limma returned only positive logFC values
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
Comment: ChatGPT optimized for bioinformatics questions
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Recent Awards •
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Popular Question
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chi.delta
▴ 40
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Sasha
▴ 270
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lait
▴ 170
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130k
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blur
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Recent Replies
Comment: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
Since the input file is named `normalized.csv` and the values look like floats most likely the counts have been already normalized somehow.
Comment: Embryo transcriptome
by
Basti
★ 1.6k
https://www.ebi.ac.uk/ena/browser/view/PRJEB11202 https://www.ebi.ac.uk/ena/browser/view/PRJNA153427
Comment: ChatGPT optimized for bioinformatics questions
by
ATpoint
72k
How is it trained on PubMed/papers? One major drawback of ChatGPT is that it wildly makes up papers that do not even exist but with great c…
Answer: sgRNA design
by
ATpoint
72k
gRNAs are single-stranded and by this they have a strand-specificity (depends where the PAM is) and that gives them an orientation.
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
ATpoint
72k
You have commas as decimal delimiters which interpreted as text. Just replace by dot and make numeric: ```r d <- data.frame(A=c("1,2", "3,…
Comment: snps from empty well, Illumina Sequencing
by
GenoMax
130k
> I receive illumina sequencing files with 96 wells, our lab leaves one > well empty. When I process the files with a SNP calling pipeline …
Answer: counts matrix should be numeric, currently it has mode: character when using a c
by
Darked89
4.4k
You can try: counts_data <- read.csv2("normalized.csv", header = TRUE) But as far as I know DESeq2 requires raw counts as inpu…
Comment: Is there bioinformatics tool to check cross hybridization between primers and pr
by
Tawny
▴ 180
Was a tool ever found for this? I am curious.
Comment: Is the Kruskal-Wallis test appropriate for genomic distances?
by
ATpoint
72k
I never used it myself so far, but I would proably look into https://bioconductor.org/packages/devel/bioc/vignettes/nullranges/inst/doc/nul…
Comment: ChatGPT optimized for bioinformatics questions
by
GenoMax
130k
Since you have kept the bot openly accessible (at least for now) this is great. People can try it out and hopefully provide feedback. I tri…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
jv
★ 1.2k
if you are doing these steps then the `R` version should be `4.1.1`. Are you sure there weren't any errors during the install of `r-base=4.…
Comment: How to use R installed by conda instead of it installed by apt on Ubuntu
by
Ram
39k
Please follow this sequence of steps and show us the outputs: ``` # Start from a fresh terminal with no conda environment active: which -a…
Comment: ChatGPT optimized for bioinformatics questions
by
Ram
39k
Happy to help!
Comment: phage genome submission in ncbi genebank
by
tahsinkhan570
• 0
Thanks for the info. I called the --compliant and later removed the Ec_number of hypothetical protein as mentioned by NCBI table2asn guidel…
Comment: ChatGPT optimized for bioinformatics questions
by
Sasha
▴ 270
Great use case - we'll take a look. Thanks for trying it out!
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