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1,000 results • Page
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Job:
Associate Professor, Ecology
Ecology
updated 20 minutes ago by
Ram
39k • written 55 minutes ago by
jterakita
▴ 20
0
votes
0
replies
21
views
What does "OS_CNSR" and "PFS_CNSR" mean?
survival
cancer
r
updated 17 minutes ago by
Ram
39k • written 1 hour ago by
JACKY
▴ 100
0
votes
0
replies
11
views
CIBERSORT Error: File not found
CIBERSORT
1 hour ago by
jcara514
• 0
2
votes
2
replies
93
views
retaining only the clusters of interest
seurat
single-cell
scRna-seq
updated 2 hours ago by
Ram
39k • written 3 hours ago by
shamza
• 0
0
votes
2
replies
171
views
Diff Bind Questions
DiffBind
CHiP-Seq
updated 4 hours ago by
Ram
39k • written 1 day ago by
B.N.
• 0
744
votes
162
replies
114k
views
101 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 5 weeks ago by
Biostar
1.8k • written 6.5 years ago by
Istvan Albert
98k
0
votes
3
replies
114
views
Gviz Coverage Plots
gviz
scrnaseq
cellranger
r
updated 22 minutes ago by
Ram
39k • written 6 hours ago by
Researcher
• 0
6
votes
6
replies
242
views
Contigs to chromosomes annotation
Assembly
mapping
contigs
updated 4 hours ago by
GenoMax
129k • written 17 hours ago by
alexandru.bologa.marian
▴ 50
2
votes
2
replies
162
views
Gene prediction software
pseudogene
gene
prediction
masking
updated 8 hours ago by
Darked89
4.4k • written 16 hours ago by
subashini.fbtpb106
▴ 10
0
votes
4
replies
178
views
Limma returned only positive logFC values
edgeR
differential-expression
deg
limma
5 hours ago by
melissachua90
▴ 40
1
vote
0
replies
58
views
Alternative approach to rarefying in 16S rRNA analysis
16S
Rarefying
rRNA
9 hours ago by
zhangdengwei
▴ 190
0
votes
1
reply
71
views
phage genome submission in ncbi genebank
phage
table2asn
ncbi
updated 2 hours ago by
acvill
▴ 290 • written 9 hours ago by
tahsinkhan570
• 0
2
votes
3
replies
183
views
Same GEO Accession, different SRR number, how to download this RNA-seq paired-end data?
sra-toolkit
fastq
RNA-seq
SRA
updated 8 hours ago by
GenoMax
129k • written 9 hours ago by
ev97
• 0
0
votes
0
replies
71
views
Which is the minor allele in ped file in plink?
plink
updated 11 hours ago by
GenoMax
129k • written 11 hours ago by
khn
▴ 130
0
votes
2
replies
114
views
Correct way to remove Nextera adapters from ITS sequences
adapters
ITS
trimmomatic
1 hour ago by
mattze731
▴ 10
1
vote
1
reply
220
views
Assigned taxonomy after dada2 only "NAs" or "Mitochondria"
16S
dada2
DECIPHER
ITS
taxonomy
12 hours ago by
mattze731
▴ 10
0
votes
0
replies
69
views
What statistical test should I use to analyse my two set of transcriptomique data?
transcriptome
12 hours ago by
F.Bedjou
▴ 10
0
votes
0
replies
67
views
Tutorial:
How to start disease research quickly and easily?
proteins
pathways
disease
research-design
genes
12 hours ago by
Coremine Medical
▴ 10
2
votes
1
reply
121
views
Visualizing Graph Alignment Format via minigraph
graph
gaf
minigraph
alignment
updated 13 hours ago by
colindaven
4.9k • written 1 day ago by
ivazirabad
▴ 20
0
votes
2
replies
204
views
Stratified sample assignment for analysis
experimental-design
stratification
updated 13 hours ago by
ATpoint
72k • written 4 days ago by
fr
▴ 200
1
vote
2
replies
219
views
What kind of statistical test does Cellranger count use?
scRNAseq
10X
Single-Cell
updated 14 hours ago by
fracarb8
▴ 950 • written 1 day ago by
hannah
• 0
3
votes
7
replies
4.1k
views
Getting Pairwise Sequence Alignment Score With Biopython
biopython
alignment
clustalw
updated 12 hours ago by
Jonathan Lefebre
▴ 70 • written 11.5 years ago by
Lakshmi
• 0
0
votes
0
replies
56
views
Difference MITOS WebServer and MITOS 2 Webserver
MITOS2
WebServer
Difference
MITOS
15 hours ago by
hashim.rana11
▴ 20
2
votes
4
replies
227
views
Get relationships and hierarchies for GO terms
GO-terms
Gene-onthology
updated 14 hours ago by
Alexander
▴ 70 • written 1 day ago by
DanielEB_fisk
▴ 10
0
votes
0
replies
87
views
Integrate RDS files
integration
23 hours ago by
Andy
▴ 50
6
votes
17
replies
4.5k
views
8 follow
Eigen genes using WGCNA
wgcna
eigengenes
updated 1 day ago by
chaco001
▴ 40 • written 4.7 years ago by
shivangi.agarwal800
▴ 120
7
votes
6
replies
267
views
Italicise annotations with pheatmap
R
Pheatmap
updated 16 hours ago by
ATpoint
72k • written 1 day ago by
jamie.pike
▴ 80
1
vote
3
replies
391
views
NanoSim Error "Please specify the training reads and its reference genome!"
NanoSim
RNA-seq
LongRead
1 day ago by
akainth
▴ 10
0
votes
1
reply
126
views
Information on sequin RNA spike in standards
Sequin
Spike-in
RNA-seq
updated 1 day ago by
Ram
39k • written 1 day ago by
akainth
▴ 10
0
votes
8
replies
5.8k
views
Bedtools problem : It looks as though you have less than 3 columns at line: 1. Are you sure your files are tab-delimited
bedtools
fasta
updated 1 day ago by
Michael
• 0 • written 3.6 years ago by
Tomm
• 0
0
votes
4
replies
1.7k
views
Spatial transcriptomics without the h5 file
h5
spatial-transcriptomics
updated 1 day ago by
Ram
39k • written 17 months ago by
jordi.diaz-manera
▴ 10
1
vote
9
replies
260
views
Trying to edit VCF file
VCF
R
bcftools
snpsaurus
updated 1 day ago by
Ram
39k • written 1 day ago by
peavy
• 0
2
votes
2
replies
220
views
Is it possible to add a dendrogram as a top annotation using ComplexHeatmap ?
Dendrogram
R
Heatmap
ComplexHeatmap
updated 1 day ago by
jv
★ 1.2k • written 2 days ago by
Manuel
• 0
0
votes
1
reply
357
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
198
views
Is hg38 on the multiz 30-way alignment inaccurate?
maf
UCSC
PHAST
multiz
1 day ago by
Daniel
▴ 30
0
votes
2
replies
1.3k
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
80
views
Label free quantification in Proteome discoverer software
proteomics
quantification
spectrometry
shotgun
1 day ago by
eqoa45
• 0
3
votes
3
replies
300
views
Perl. How to retrieve data until a keyword in GenBank?
fasta
sequence
GenBank
perl
1 day ago by
Fungi-Beware!
▴ 10
0
votes
1
reply
139
views
CHiP-Seq Questions
DiffBind
CHiP-Seq
updated 1 day ago by
jared.andrews07
★ 14k • written 1 day ago by
B.N.
• 0
1
vote
0
replies
87
views
How to predict gene amplification from RNAseq and ATACseq data?
amplification
ATAC
1 day ago by
Dan
▴ 120
6
votes
7
replies
318
views
NCBI API, Perl
API
NCBI
updated 1 day ago by
GenoMax
129k • written 1 day ago by
alessandro.alma00
• 0
1
vote
2
replies
150
views
hisat2 Error 137
hisat2
RNA-seq
1 day ago by
Forough
▴ 10
0
votes
0
replies
88
views
Error occured at the PHG imputation step: allele in genotype not in the variant context
PHG
Imputation
PracticalHaplotypeGraph
Haplotype
1 day ago by
xeod21
• 0
1
vote
0
replies
109
views
Herald:
The Biostar Herald for Monday, June 05, 2023
herald
1 day ago by
Biostar
1.8k
2
votes
1
reply
128
views
Is RNA-Seq well suited for studying pseudogenes and lncRNA?
rna
ncRNA
transcriptome
pseudogene
rna-seq
updated 1 day ago by
rpolicastro
12k • written 1 day ago by
Kermit
▴ 80
2
votes
5
replies
266
views
Embryo transcriptome
database
transcriptome
SRA
updated 1 day ago by
ATpoint
72k • written 1 day ago by
firefox91
• 0
1
vote
3
replies
164
views
Obtain a --gene-trans-map file after rnaSPAdes
rnaSPAdes
Trinity
1 day ago by
UserA
• 0
1
vote
0
replies
106
views
Tutorial:
Get a list of genes associated with a drug in 1 min
drug
genes
drug-targets
updated 1 day ago by
Ram
39k • written 1 day ago by
Coremine Medical
▴ 10
2
votes
3
replies
267
views
Getting species names and taxa id from assembly accession number
efetch
biopython
entrez
updated 1 day ago by
MirianT_NCBI
▴ 600 • written 2 days ago by
kwhiggins27
▴ 10
0
votes
0
replies
81
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 1 day ago by
beausoleilmo
▴ 530
1,000 results • Page
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C: Regarding filter primary alignment
Alternative approach to rarefying in 16S rRNA analysis
Answer: Gene prediction software
Comment: retaining only the clusters of interest
Comment: retaining only the clusters of interest
Calculating read abundances across MAGs (question)
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Recent Replies
Comment: calculate p value and associated z score for snp-gene pair
by
rheab1230
▴ 140
Thank you so much for the information.
Comment: Gviz Coverage Plots
by
Ram
39k
I understand that but stick to one place at least for a while and always link to other places you've posted (reasonable places, we don't ne…
Comment: Gviz Coverage Plots
by
Researcher
• 0
Sorry, I didn't know that posting it on another forum was rude but I really need help with this.
Comment: Correct way to remove Nextera adapters from ITS sequences
by
mattze731
▴ 10
Trimmomatic allows to enter custom adapter sequences, but I don't see how this would change the outcome. Similarly, trimmomatic also allows…
Comment: phage genome submission in ncbi genebank
by
acvill
▴ 290
When running prokka, did you call the `--compliant` parameter to enforce Genbank compliance? https://github.com/tseemann/prokka#ncbi-genban…
Comment: Correct way to remove Nextera adapters from ITS sequences
by
Trivas
★ 1.2k
Some of these programs have a minimum size threshold for a read to be retained. You could play around with that to keep all trimmed reads 5…
Comment: retaining only the clusters of interest
by
seidel
11k
Could it be that idents needs a character string instead of integers? Also, you have an extra comma in your call after c(0:16).
Comment: retaining only the clusters of interest
by
Ram
39k
`idents` is probably a factor so even though you've removed cells with those level values, the factor level still remains. Don't worry abou…
Comment: Contigs to chromosomes annotation
by
GenoMax
129k
I would still recommend using `minimap2` and aligning against reference. It should go pretty fast. You can either work with PAF (default) f…
Comment: Diff Bind Questions
by
Ram
39k
I've moved this to a comment as it does not directly answer OP's question.
Comment: Diff Bind Questions
by
Daniel
▴ 30
I'm very new myself and there's plenty of people who can answer your question better than I can, but here is a resource I found extremely h…
Comment: Contigs to chromosomes annotation
by
alexandru.bologa.marian
▴ 50
If the number of contigs was so small I would manually check each alignment and edit the header of each contig,inserting the corresponding …
Comment: Gviz Coverage Plots
by
Ram
39k
Do not post on multiple fora just because you want a fast response, it's plain rude. At least point to the other post so we know you're ask…
Comment: Limma returned only positive logFC values
by
melissachua90
▴ 40
No the library sizes across conditions should be relatively homogenous because it's from the same dataset. I clustered the samples into sub…
Comment: Limma returned only positive logFC values
by
LChart
2.6k
It shouldn't, unless there's a misspecification in design. Is it the case that the library sizes are very different between the conditions …
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