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121,012 results • Page
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Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
CancerPhylogenetics
ChromosomalInstability
10 hours ago by
Bingxin
• 0
0
votes
1
reply
158
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 22 hours ago by
Jasim
• 0 • written 2 days ago by
omicon
▴ 40
1
vote
3
replies
317
views
Proper preprocessing for ML after limma, quantile normalization and log2 transformation: Is standardization still necessary?
featureselection
microarray
preprocessing
updated 1 day ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Sib
▴ 60
0
votes
0
replies
85
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 22 hours ago by
GenoMax
150k • written 1 day ago by
Abieskawa
• 0
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 8 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
3
replies
283
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 1 day ago by
Mensur Dlakic
★ 29k • written 1 day ago by
Novoo
• 0
1
vote
1
reply
209
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 10 hours ago by
Michael
55k • written 3 days ago by
Chatchapon
• 0
1
vote
4
replies
252
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 1 day ago by
Mensur Dlakic
★ 29k • written 1 day ago by
vladimir_vinarsky
• 0
0
votes
2
replies
171
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
1 day ago by
andrebolerbarros
• 0
0
votes
4
replies
308
views
UCSC's NCBI RefSeq Track tables: header differences
ucsc-genome-browswer
refseq
ncbi
2 days ago by
Synanth
• 0
2
votes
2
replies
1.3k
views
How do you do differential splicing using edgeR command diffSpliceDGE?
differential-splicing
diffSpliceDGE
edger
updated 2 days ago by
Gordon Smyth
★ 7.9k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.9k
0
votes
0
replies
142
views
sequenced noise elimination in searching for snp
snp
sequencing
virus
3 days ago by
gagi1993
• 0
0
votes
1
reply
205
views
Issue with Agilent 2100 BioAnalyzer HS DNA Assay Trace
library-preparation
DNA
bioanalyzer
updated 2 days ago by
GenoMax
150k • written 3 days ago by
Beatrice
• 0
1
vote
2
replies
726
views
QIAseq 16S/ITS Screening Panel Primers?
16s
primers
metagenomics
ITS
updated 3 days ago by
GenoMax
150k • written 3.2 years ago by
Isaac
• 0
2
votes
1
reply
259
views
Analysing gene CNV from TCGA using TCGAbiolinks
TCGA
updated 3 days ago by
Zhenyu Zhang
★ 1.3k • written 4 days ago by
Matt
• 0
1
vote
3
replies
305
views
How to use LOEUF plugin in VEP?
LOEUF
VEP
updated 3 days ago by
GenoMax
150k • written 4 days ago by
Sd
• 0
0
votes
0
replies
271
views
Trouble with CIBERSORTx: All P-values > 0.05, Low Correlation, High RMSE – What Could Be Going Wrong?
R
CIBERSORTx
CIBERSORT
script
updated 3 days ago by
GenoMax
150k • written 3 days ago by
Pumla
• 0
0
votes
1
reply
196
views
How can I identify genes with the MSTRG notation?
R
stringtie
RNA-Seq
updated 3 days ago by
GenoMax
150k • written 3 days ago by
pinheirofabiano
▴ 110
0
votes
0
replies
918
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 3 days ago by
ATpoint
87k • written 3 days ago by
kayah
▴ 20
1
vote
3
replies
288
views
Visualise duplications and inversions
inversions
duplications
updated 2 days ago by
cmdcolin
★ 4.2k • written 3 days ago by
priya.bmg
▴ 70
1
vote
1
reply
218
views
Exon-level counts via featureCounts
diffSpliceDGE
exon
RNASeq
featureCounts
edgeR
updated 3 days ago by
GenoMax
150k • written 3 days ago by
n_navy
• 0
0
votes
5
replies
315
views
Picard : Bait_interval and Target_interval
Picard
Bed
read-depth
coverage
updated 3 days ago by
Ram
45k • written 3 days ago by
AIMAR
• 0
3
votes
2
replies
258
views
Does vg giraffe output secondary and supplimentary alignments?
vg
giraffe
4 days ago by
lushjia
• 0
0
votes
0
replies
193
views
Question about Calculation of Dietary index in the NHANES Database
index
DI-GM
Dietary
NHANES
4 days ago by
城玮
• 0
0
votes
1
reply
288
views
Detection SNPs and Indels Bacteria
SNPs
updated 4 days ago by
Istvan Albert
102k • written 5 days ago by
Eltercertopico
• 0
1
vote
4
replies
468
views
protease candidates for my protein of interest
cleaving-site
proteases
protein
4 days ago by
Fatemeh
▴ 40
1
vote
3
replies
338
views
Different number of fragments after doublets removal in each run
ArchR
3 days ago by
Bioinformatics_16
• 0
1
vote
2
replies
289
views
Seeking Guidance on Next Steps for DNA Methylation Biomarker Screening in Cancer Prognosis
early-cancer-screening
TCGA
Epigenomics
DNA-Methylation
cancer-prognosis
3 days ago by
Riley J
• 0
0
votes
1
reply
267
views
Help with Panel of Normal (PON)
somatic-mutation
PoN
updated 4 days ago by
Ram
45k • written 5 days ago by
TJ
• 0
8
votes
5
replies
517
views
6 follow
Why don't I see people calculating FPKM from normalized read counts?
normalization
RNA-seq
updated 18 hours ago by
kalavattam
▴ 350 • written 5 days ago by
shelkmike
★ 1.5k
1
vote
9
replies
669
views
Error during running wf-bacterial-genome (nextflow run epi2me-labs/wf-bacterial-genomes).
EPI2ME
MEDAKA
updated 2 days ago by
GenoMax
150k • written 5 days ago by
Anurag
• 0
0
votes
0
replies
195
views
freebayes with pools of different number of individuals
freebayes
poolseq
5 days ago by
Jeanlain
• 0
0
votes
3
replies
320
views
Insight into Trimmomatic
Trimmomatic
Trimming
Reads
updated 5 days ago by
GenoMax
150k • written 5 days ago by
jh5ym
• 0
1
vote
3
replies
342
views
Trouble when uploading FASTQ files on NCBI
rnaseq
ncbi
3 days ago by
Gerard
▴ 20
1
vote
4
replies
384
views
SyntaxError in file /snakefile, line 22: invalid decimal literal: None
python
snakemake
updated 4 days ago by
Jesse
▴ 870 • written 5 days ago by
Ana
▴ 10
3
votes
2
replies
374
views
News:
Building an mmCIF parser for enzyme structure analysis — feedback & ideas welcome!
mmcif
5 days ago by
Shravya
• 0
0
votes
0
replies
234
views
News:
Course: Introduction to Genome Annotation (Online, 19–22 May 2025)
Gene-Prediction
Genome-Annotation
Gene-Models
6 days ago by
Physalia-courses
★ 2.6k
0
votes
1
reply
275
views
Error with running cellranger-atac count
cellranger
atac
single-cell
updated 5 days ago by
Ram
45k • written 6 days ago by
Khôi
• 0
0
votes
2
replies
344
views
HIC-pro with Forward and reverse reads not paired even when I use their test data.
HIC-pro
5 days ago by
Aki
▴ 20
1
vote
1
reply
439
views
Using DEXseq on kallisto tsv outputs ?
alignement
DEXseq
kallisto
updated 6 days ago by
Gordon Smyth
★ 7.9k • written 11 days ago by
Gerard
▴ 20
0
votes
0
replies
288
views
Job:
2025 Arrowhead AI/LLM for Computational Biology and Data Science Internship
intern
updated 6 days ago by
GenoMax
150k • written 6 days ago by
Shicheng Guo
★ 9.6k
1
vote
2
replies
635
views
ChIP-seq gene blacklist for Rattus norvegicus
rat
blacklist
ChIP-seq
updated 6 days ago by
GenoMax
150k • written 12 months ago by
Thomas
• 0
4
votes
10
replies
987
views
6 follow
Extract length of sample sequence from vcf
microsatellites
bcftools
vcf
indels
variants
updated 6 days ago by
cmdcolin
★ 4.2k • written 16 days ago by
jahnreinhard.ringger
• 0
0
votes
0
replies
266
views
Tutorial:
Fast SCENIC GRN Analysis with RegDiffusion
GRN
network
scRNA-seq
wgcna
6 days ago by
Hao
▴ 10
2
votes
3
replies
783
views
Is it reasonable to do "Gene Regulatory Network Inference" for each cell type and do differential GRN
GRN
scRNA-seq
updated 6 days ago by
Hao
▴ 10 • written 2.6 years ago by
shangguandong1996
▴ 30
1
vote
2
replies
542
views
Blastx issue
blastx
lncRNA
updated 5 days ago by
Ram
45k • written 9 days ago by
Avik
• 0
2
votes
9
replies
748
views
TPM vs FPKM divergence at high values
tpm
fpkm
normalisation
updated 5 days ago by
Istvan Albert
102k • written 9 days ago by
megancgrdnr
• 0
3
votes
0
replies
283
views
Herald:
The Biostar Herald for Monday, April 14, 2025
herald
6 days ago by
Biostar
3.5k
1
vote
2
replies
438
views
What is the best way to know if a pair of genes is random?
go-terms
genes
updated 5 days ago by
Ram
45k • written 9 days ago by
Ana
▴ 10
1
vote
1
reply
394
views
How to save the AlphaFold PAE plot as an image in ChimeraX using command line ?
PAE
ChimeraX
AlphaFold
updated 6 days ago by
LauferVA
4.7k • written 8 days ago by
Picasa
▴ 680
121,012 results • Page
1 of 2421
Recent Votes
Answer: Analysing gene CNV from TCGA using TCGAbiolinks
Answer: Any recommendation for calculating Fu and Li's D using RStudio?
Answer: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
C: Why Is Gwas Underpowered To Detect Association In Rare Variants?
C: Why Is Gwas Underpowered To Detect Association In Rare Variants?
A: Why Is Gwas Underpowered To Detect Association In Rare Variants?
A: Why Is Gwas Underpowered To Detect Association In Rare Variants?
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3.9k
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Recent Replies
Comment: Why don't I see people calculating FPKM from normalized read counts?
by
kalavattam
▴ 350
Thank you for correcting me. I've updated the post.
Comment: miRNA alignment and count generation
by
Jasim
• 0
I am also in the same boat bro, i got 000 countfeauture after aligned. After truobleshooting I found that sam file was failed. My sample wa…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
Mensur Dlakic
★ 29k
My recommendation is to take a couple of days and research what is already available. Is it more productive to spend a week and test severa…
Comment: Running out of disc space with wsl2
by
Mensur Dlakic
★ 29k
I think there is a certain requirement for temporary disk space during prefetch, and you are likely blowing through it by running this in p…
Answer: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Mensur Dlakic
★ 29k
> However, since ML algorithms like KNN, SVM, and NN are sensitive to feature scale and for PCA-based feature extraction, standardization i…
Comment: Why don't I see people calculating FPKM from normalized read counts?
by
dsull
★ 7.3k
Bo Li and Colin Dewey (the developers of RSEM) introduced TPM in 2009 even before the cufflinks paper introduced FPKM. https://academic.oup…
Comment: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
Novoo
• 0
Thanks so much for the thoughtful feedback—I really appreciate you laying out the practical challenges. Here’s how I’m addressing each of y…
Comment: Running out of disc space with wsl2
by
vladimir_vinarsky
• 0
Thank you, I have 32GB rRAM, 16 Cores, Threads 32, and some 120GB on the C:\ drive (which is the SSD). I think the download and processi…
Comment: Filtering vcf file for variants - including non-selected variants
by
andrebolerbarros
• 0
Hey @yokofakun! Thanks for your answer. Unfortunately, this does not seem to work as well... I had to use the variant list with `-T` cri…
Answer: Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
by
GenoMax
150k
> student working on a lightweight lab data management & analytics tool aimed at small academic and startup labs Commendable aim. Wishing …
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
Sib
▴ 60
That question was about the need or lack of need to perform log transformation. This question is about the need or lack of need to standard…
Comment: Proper preprocessing for ML after limma, quantile normalization and log2 transfo
by
GenoMax
150k
Prior thread for reference : https://www.biostars.org/p/9611266/
Answer: Any recommendation for calculating Fu and Li's D using RStudio?
by
Michael
55k
I have recently experienced the same, also PopGenome was thrown out of CRAN a while ago. You might get it to work in combination with an ol…
Comment: Running out of disc space with wsl2
by
GenoMax
150k
How many cores, how much RAM and disk space do you have on this computer? WSL2 allocates a TB of disk space so as long as you have the reso…
Comment: Running out of disc space with wsl2
by
Arup Ghosh
3.3k
It depends on how much data you are trying to download and the storage space left on your PC's `C:\` drive, as it's the default location fo…
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