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121,032 results • Page
1 of 2421
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Votes
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0
votes
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68
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how to handle infinite M-values in methylation array data
M-value
methylation
infinite
array
updated 49 minutes ago by
Basti
★ 2.1k • written 13 hours ago by
matt192
• 0
1
vote
3
replies
1.6k
views
Free and redistributable genomic data sets?
data
software-development
genomics
updated 2 hours ago by
Meeru
• 0 • written 9.2 years ago by
woemler
▴ 170
1
vote
4
replies
934
views
Rna-seq data
data
rna-seq
updated 4 hours ago by
ehaag
▴ 20 • written 3.1 years ago by
biology_inform
▴ 50
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 11 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
6
votes
3
replies
839
views
RNAseq example data
expression
RNA-Seq
data
next-gen
updated 4 hours ago by
ehaag
▴ 20 • written 4.6 years ago by
rakinitopo
▴ 10
0
votes
1
reply
202
views
Transcript_id with "-0" after "flair collapse"
flair
updated 5 hours ago by
cheong
• 0 • written 5 months ago by
anna_shin
• 0
0
votes
0
replies
52
views
Can I use glucose measured using two different devices in my study?
normalization
standardization
transformation
10 hours ago by
Faith
▴ 50
0
votes
1
reply
86
views
Limma model gives weird results
model
multivariate
Limma
updated 10 hours ago by
Gordon Smyth
★ 7.9k • written 12 hours ago by
leranwangcs
▴ 150
1
vote
3
replies
589
views
Snakemake - pipeline shut down without error
snakemake
13 hours ago by
bhumm
▴ 200
0
votes
1
reply
98
views
Source for `transcript_name` in GTFs
GTF
updated 15 hours ago by
GenoMax
150k • written 16 hours ago by
gernophil
▴ 120
5
votes
5
replies
237
views
Tool:
Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and de-duplication using cutadapt
rad-seq
ddRADseq
demultiplexing
deduplication
17 hours ago by
Rafal
▴ 10
0
votes
2
replies
103
views
How to normalised DNA sequencing depth for genomic variant discovery ?
normalisation
read-depth
variant-calling
updated 17 hours ago by
Ram
45k • written 18 hours ago by
AIMAR
• 0
2
votes
4
replies
189
views
RNASeq featureCounts Help Needed
fungi
featurecounts
RNASeq
18 hours ago by
SomeOne
▴ 170
0
votes
0
replies
75
views
PAUP* error with exporting result file
PAUP
SVDquartet
20 hours ago by
ylkim9
• 0
0
votes
1
reply
95
views
I need to convert Axiom output to PLINK format I did not find annotation.db
Axiom
PLINK
apt-format-result
updated 18 hours ago by
GenoMax
150k • written 20 hours ago by
AlmuhayyaA
• 0
0
votes
3
replies
155
views
How to merge heterogeneously normalized RNA-seq datasets for meta-analysis?
normalization
rna-seq
updated 28 minutes ago by
ATpoint
87k • written 23 hours ago by
pipelinfections
• 0
0
votes
0
replies
92
views
Tool:
I packaged some tools in python pypi for Windows (fastqc, bowtie2, samtools)
python
pypi
5 hours ago by
Cris
• 0
0
votes
3
replies
261
views
Transcript ID
id
transcript
updated 1 day ago by
Meeru
• 0 • written 2 days ago by
cheong
• 0
0
votes
1
reply
133
views
Galaxy + RStudio
R
RNA-seq
RStudio
updated 1 day ago by
swbarnes2
14k • written 1 day ago by
justus
• 0
8
votes
18
replies
3.1k
views
8 follow
How to limit fasta header to 40 characters?
unix
seqkit
fasta
updated 1 day ago by
jena
▴ 320 • written 19 months ago by
fishingline37
• 0
1
vote
2
replies
191
views
Transcript level quantification and gene length scaling for rRNA depleted libraries
RNASeq
updated 1 day ago by
dsull
★ 7.4k • written 1 day ago by
marc.zimmerli
▴ 10
0
votes
0
replies
108
views
Model diagnostics for GAM (Generalised Additive Model)
gam
mgcv
generalized-additive-model
1 day ago by
Tuấn Anh
• 0
2
votes
5
replies
583
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 1 day ago by
Darked89
4.7k • written 4 days ago by
Novoo
▴ 10
1
vote
1
reply
166
views
landscape of RNA types and their functions/ scRNA
transcriptomics
scRNA
biology
updated 1 day ago by
ATpoint
87k • written 1 day ago by
Ariadna
▴ 20
1
vote
2
replies
152
views
Is vg toolkit suitable for haplotype calling?
pangenome
haplotype
vg
6 minutes ago by
Pau
• 0
0
votes
0
replies
105
views
Dfam annotations
dfam
1 day ago by
frarodmar17
• 0
0
votes
3
replies
374
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 1 day ago by
i.sudbery
21k • written 5 days ago by
omicon
▴ 40
1
vote
2
replies
208
views
Cytoscape Node Size Mapping
Cytoscape
2 days ago by
William
▴ 20
1
vote
2
replies
253
views
Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
2 days ago by
RJDan
• 0
0
votes
3
replies
801
views
HOMER Motif Analysis-- homer2 error
rna-seq
homer
updated 2 days ago by
ATpoint
87k • written 15 months ago by
HypoGG
• 0
4
votes
0
replies
187
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
2 days ago by
Biostar
3.5k
0
votes
4
replies
264
views
Forum:
ELISA‑Focused Lab Management & Analysis App – Would You Use It?
biotech
startup
updated 2 days ago by
Ram
45k • written 2 days ago by
Novoo
▴ 10
0
votes
0
replies
208
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
Cancer-Phylogenetics
Chromosomal-Instability
updated 1 day ago by
Ram
45k • written 3 days ago by
Bingxin
• 0
1
vote
10
replies
834
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
updated 16 hours ago by
Mensur Dlakic
★ 29k • written 4 days ago by
Sib
▴ 60
0
votes
0
replies
205
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 3 days ago by
GenoMax
150k • written 4 days ago by
Abieskawa
• 0
1
vote
1
reply
342
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 3 days ago by
Michael
55k • written 6 days ago by
Chatchapon
• 0
1
vote
4
replies
432
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 4 days ago by
Mensur Dlakic
★ 29k • written 4 days ago by
vladimir_vinarsky
• 0
0
votes
2
replies
290
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
4 days ago by
andrebolerbarros
• 0
0
votes
4
replies
438
views
UCSC's NCBI RefSeq Track tables: header differences
ucsc-genome-browswer
refseq
ncbi
5 days ago by
Synanth
• 0
3
votes
2
replies
1.4k
views
How do you do differential splicing using edgeR command diffSpliceDGE?
differential-splicing
diffSpliceDGE
edger
updated 5 days ago by
Gordon Smyth
★ 7.9k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
259
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
6 days ago by
gagi1993
• 0
0
votes
1
reply
316
views
Issue with Agilent 2100 BioAnalyzer HS DNA Assay Trace
library-preparation
DNA
bioanalyzer
updated 5 days ago by
GenoMax
150k • written 6 days ago by
Beatrice
• 0
1
vote
2
replies
839
views
QIAseq 16S/ITS Screening Panel Primers?
16s
primers
metagenomics
ITS
updated 6 days ago by
GenoMax
150k • written 3.2 years ago by
Isaac
• 0
3
votes
2
replies
438
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
1 day ago by
Matt
• 0
1
vote
3
replies
425
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
updated 6 days ago by
GenoMax
150k • written 7 days ago by
Sd
• 0
0
votes
0
replies
437
views
Trouble with CIBERSORTx: All P-values > 0.05, Low Correlation, High RMSE – What Could Be Going Wrong?
R
CIBERSORTx
CIBERSORT
script
updated 6 days ago by
GenoMax
150k • written 6 days ago by
Pumla
• 0
0
votes
1
reply
310
views
How can I identify genes with the MSTRG notation?
R
stringtie
RNA-Seq
updated 6 days ago by
GenoMax
150k • written 6 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
1.6k
views
dittoHeapmap didn't work in my data set(error code :Error in .subscript.2ary(x, i, j, drop = TRUE) : subscript out of bounds)
dittoseq
scRNAseq
updated 6 days ago by
ATpoint
87k • written 6 days ago by
kayah
▴ 20
1
vote
3
replies
410
views
Visualise duplications and inversions
inversions
duplications
updated 5 days ago by
cmdcolin
★ 4.2k • written 6 days ago by
priya.bmg
▴ 70
1
vote
3
replies
416
views
Exon-level counts via featureCounts
diffSpliceDGE
exon
RNASeq
featureCounts
edgeR
updated 2 days ago by
rfran010
★ 1.4k • written 6 days ago by
n_navy
• 0
121,032 results • Page
1 of 2421
Recent Votes
How to create a phylogenetic tree from 30 VCF files
Answer: Snakemake - pipeline shut down without error
Answer: Getting sequences from fastq file using Grep command
Comment: RNASeq featureCounts Help Needed
Comment: RNASeq featureCounts Help Needed
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
Comment: Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and
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Comment: Is vg toolkit suitable for haplotype calling?
by
Pau
• 0
What I mean is: from a set of long reads and a pangenome with no haplotype paths (because it was built with unphased vcf) obtain the differ…
Comment: How to merge heterogeneously normalized RNA-seq datasets for meta-analysis?
by
ATpoint
87k
Because data are heterogeneous, on entirely different scales, assay (vastly) different amounts of genes and are inherently incomparable qua…
Answer: how to handle infinite M-values in methylation array data
by
Basti
★ 2.1k
This is a known problem happening with some of the normalization methods. As long as the detection P-value is ok, you can keep these probes…
Answer: Free and redistributable genomic data sets?
by
Meeru
• 0
Yes, check out RefSeq (NCBI), Ensembl, and UCSC Genome Browser they offer genomic data under permissive licenses that generally allow redis…
Comment: promoter and insulator data download
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ehaag
▴ 20
You can find promoter and insulator data or other gene expression data in the NIAID Data Ecosystem: https://data.niaid.nih.gov/ The interf…
Answer: Free and redistributable genomic data sets?
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ehaag
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You can use the NIAID Data Ecosystem to search for genomic data: https://data.niaid.nih.gov/ And you can filter results by conditions of…
Answer: Rna-seq data
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ehaag
▴ 20
The NIAID Data Ecosystem allows you to search across dozens of repositories (including GEO, but about 40 others as well) to find RNA-seq da…
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The NIAID Data Ecosystem has a searchable interface for finding biomanufacturing data, as well as data related to drug trials, pharmaceutic…
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You can find a huge amount of data including RNA-seq expression data using the NIAID Data Ecosystem's searchable interface: https://data.ni…
Answer: Transcript_id with "-0" after "flair collapse"
by
cheong
• 0
Hi anna, do you know the answer now? Thanks.
Comment: Limma model gives weird results
by
Gordon Smyth
★ 7.9k
The code that you show cannot be correct, because the `topTable` `coef` refers to a term that is not in the design matrix. The code as show…
Comment: How to merge heterogeneously normalized RNA-seq datasets for meta-analysis?
by
pipelinfections
• 0
Could you please elaborate on why you would never combine them into a single table? There are several papers that do this, e.g. [this one][…
Answer: Snakemake - pipeline shut down without error
by
bhumm
▴ 200
Circling back to answer my own question. After testing the `--dry-run` (as @Shred suggested) it completed as expected. The rule that consis…
Answer: Source for `transcript_name` in GTFs
by
GenoMax
150k
Manual annotation is done by `HAVANA` group from Ensembl: https://www.ensembl.org/info/genome/genebuild/manual_havana.html It would be fair…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Mensur Dlakic
★ 29k
> Additionally, I’d greatly appreciate your insights on how to handle this issue for KNN, PCA, and Relief? I again refer you to what I alr…
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