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121,041 results • Page
1 of 2421
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0
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19
views
Tool:
GENetLib: A Python Library for Gene–environment Interaction Analysis via Deep Learning
gene-environment
interaction
analysis
1 hour ago by
Barry
• 0
2
votes
5
replies
123
views
STAR vs. Kallisto
STAR
kallisto
alignment
RNA-Seq
mapping
updated 3 hours ago by
ATpoint
87k • written 4 hours ago by
gogeni5529
▴ 60
0
votes
0
replies
26
views
How to Annotate VCF with AlphaMissense Using VEP and dbNSFP v5.1a in Offline Mode?
AlphaMissense
dbNSFP
VEP
ensembl
2 hours ago by
DareDevil
★ 4.4k
0
votes
1
reply
114
views
News:
Phylogenetic Comparative Methods in R (12–16 May, Online)
R
Phylogenetic-Comparative-Methods
updated 6 hours ago by
Meeru
• 0 • written 1 day ago by
Physalia-courses
★ 2.6k
836
votes
167
replies
174k
views
111 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 12 days ago by
Biostar
3.5k • written 8.4 years ago by
Istvan Albert
102k
0
votes
1
reply
96
views
Biostar handbook
Handbook
Biostar
updated 13 hours ago by
GenoMax
150k • written 13 hours ago by
himanshu0102
• 0
2
votes
2
replies
1.3k
views
pangenome - Create a diagram venn
roary
grep
awk
pangenome
venn
updated 16 hours ago by
mplace
▴ 40 • written 2.0 years ago by
BATMAN
• 0
5
votes
4
replies
183
views
Addressing two nuisance factors in RNAseq
bulkRNAseq
updated 3 hours ago by
ATpoint
87k • written 17 hours ago by
jkim
▴ 190
0
votes
5
replies
226
views
DRAGEN FILTER
dragen
variant-calling
updated 20 hours ago by
GenoMax
150k • written 21 hours ago by
theresia.celine
• 0
1
vote
0
replies
115
views
Interpretation of the results: PCA
proteomics
PCA
4 hours ago by
Ariadna
▴ 30
3
votes
5
replies
233
views
How to check normal BAM_files before create a Panel Of Normals (PoN)
GATK
variant_calling
PoN
21 hours ago by
AIMAR
• 0
0
votes
1
reply
150
views
how to handle infinite M-values in methylation array data
M-value
methylation
infinite
array
updated 1 day ago by
Basti
★ 2.1k • written 1 day ago by
matt192
• 0
1
vote
3
replies
1.7k
views
Free and redistributable genomic data sets?
data
software-development
genomics
updated 1 day ago by
Meeru
• 0 • written 9.2 years ago by
woemler
▴ 170
1
vote
5
replies
1.0k
views
Rna-seq data
data
rna-seq
updated 23 hours ago by
GenoMax
150k • written 3.1 years ago by
biology_inform
▴ 50
6
votes
3
replies
898
views
RNAseq example data
expression
RNA-Seq
data
next-gen
updated 1 day ago by
ehaag
▴ 20 • written 4.6 years ago by
rakinitopo
▴ 10
0
votes
1
reply
255
views
Transcript_id with "-0" after "flair collapse"
flair
updated 23 hours ago by
GenoMax
150k • written 5 months ago by
anna_shin
• 0
0
votes
0
replies
97
views
Can I use glucose measured using two different devices in my study?
normalization
standardization
transformation
1 day ago by
Faith
▴ 50
0
votes
2
replies
190
views
Limma model gives weird results
model
multivariate
Limma
updated 22 hours ago by
ATpoint
87k • written 1 day ago by
leranwangcs
▴ 150
1
vote
3
replies
644
views
Snakemake - pipeline shut down without error
snakemake
1 day ago by
bhumm
▴ 200
2
votes
2
replies
194
views
Source for `transcript_name` in GTFs
GTF
updated 22 hours ago by
Jorge - Ensembl
▴ 20 • written 1 day ago by
gernophil
▴ 120
5
votes
5
replies
297
views
Tool:
Lightweight bash pipeline for ddRADseq read pre-processing, demultiplexing, and de-duplication using cutadapt
rad-seq
ddRADseq
demultiplexing
deduplication
1 day ago by
Rafal
▴ 10
0
votes
2
replies
159
views
How to normalised DNA sequencing depth for genomic variant discovery ?
normalisation
read-depth
variant-calling
updated 1 day ago by
Ram
45k • written 1 day ago by
AIMAR
• 0
2
votes
4
replies
250
views
RNASeq featureCounts Help Needed
fungi
featurecounts
RNASeq
1 day ago by
SomeOne
▴ 170
0
votes
0
replies
114
views
PAUP* error with exporting result file
PAUP
SVDquartet
1 day ago by
ylkim9
• 0
0
votes
1
reply
137
views
I need to convert Axiom output to PLINK format I did not find annotation.db
Axiom
PLINK
apt-format-result
updated 1 day ago by
GenoMax
150k • written 1 day ago by
AlmuhayyaA
• 0
1
vote
3
replies
247
views
How to merge heterogeneously normalized RNA-seq datasets for meta-analysis?
normalization
rna-seq
updated 1 day ago by
ATpoint
87k • written 2 days ago by
pipelinfections
• 0
1
vote
0
replies
146
views
Tool:
I packaged some tools in python pypi for Windows (fastqc, bowtie2, samtools)
python
pypi
1 day ago by
Cris
▴ 10
0
votes
3
replies
304
views
Transcript ID
id
transcript
updated 2 days ago by
Meeru
• 0 • written 3 days ago by
cheong
• 0
0
votes
1
reply
176
views
Galaxy + RStudio
R
RNA-seq
RStudio
updated 2 days ago by
swbarnes2
14k • written 2 days 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 2 days ago by
jena
▴ 320 • written 19 months ago by
fishingline37
• 0
1
vote
2
replies
238
views
Transcript level quantification and gene length scaling for rRNA depleted libraries
RNASeq
updated 2 days ago by
dsull
★ 7.4k • written 2 days ago by
marc.zimmerli
▴ 10
0
votes
0
replies
149
views
Model diagnostics for GAM (Generalised Additive Model)
gam
mgcv
generalized-additive-model
2 days ago by
Tuấn Anh
• 0
2
votes
5
replies
637
views
Forum:
Small‑Lab Data Management & Analytics Tool – What are your biggest pain points?
biotech
startup
updated 2 days ago by
Darked89
4.7k • written 5 days ago by
Novoo
▴ 10
1
vote
1
reply
206
views
landscape of RNA types and their functions/ scRNA
transcriptomics
scRNA
biology
updated 2 days ago by
ATpoint
87k • written 2 days ago by
Ariadna
▴ 30
1
vote
3
replies
269
views
Is vg toolkit suitable for haplotype calling?
pangenome
haplotype
vg
updated 10 hours ago by
Jordan M Eizenga
▴ 700 • written 2 days ago by
Pau
• 0
0
votes
0
replies
145
views
Dfam annotations
dfam
2 days ago by
frarodmar17
• 0
0
votes
3
replies
418
views
miRNA alignment and count generation
aligment
Mapping
Bowtie
miRNAs
updated 3 days ago by
i.sudbery
21k • written 6 days ago by
omicon
▴ 40
1
vote
2
replies
251
views
Cytoscape Node Size Mapping
Cytoscape
3 days ago by
William
▴ 20
1
vote
2
replies
297
views
Deeptools: Custom gcbias plots in R possible?
computegcbias
deeptools
3 days ago by
RJDan
• 0
0
votes
3
replies
842
views
HOMER Motif Analysis-- homer2 error
rna-seq
homer
updated 3 days ago by
ATpoint
87k • written 15 months ago by
HypoGG
• 0
4
votes
0
replies
232
views
Herald:
The Biostar Herald for Monday, April 21, 2025
herald
3 days ago by
Biostar
3.5k
0
votes
4
replies
310
views
Forum:
ELISA‑Focused Lab Management & Analysis App – Would You Use It?
biotech
startup
updated 3 days ago by
Ram
45k • written 4 days ago by
Novoo
▴ 10
0
votes
0
replies
251
views
Job:
Research Fellow in Cancer Evolution (Deadline 30 Apr 2025)
Cancer-Phylogenetics
Chromosomal-Instability
updated 2 days ago by
Ram
45k • written 4 days ago by
Bingxin
• 0
1
vote
10
replies
1.1k
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 5 days ago by
Sib
▴ 60
0
votes
0
replies
241
views
How to get gene count and transcript count from Stringtie
Stringtie
updated 5 days ago by
GenoMax
150k • written 5 days ago by
Abieskawa
• 0
1
vote
1
reply
382
views
Any recommendation for calculating Fu and Li's D using RStudio?
PopGenome
updated 4 days ago by
Michael
55k • written 7 days ago by
Chatchapon
• 0
1
vote
4
replies
480
views
Running out of disc space with wsl2
Memory
WSL2
capacity
Disc
updated 5 days ago by
Mensur Dlakic
★ 29k • written 6 days ago by
vladimir_vinarsky
• 0
0
votes
2
replies
332
views
Filtering vcf file for variants - including non-selected variants
bedtools
calling
variant
bcftools
5 days ago by
andrebolerbarros
• 0
0
votes
4
replies
489
views
UCSC's NCBI RefSeq Track tables: header differences
ucsc-genome-browswer
refseq
ncbi
6 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 6 days ago by
Gordon Smyth
★ 7.9k • written 3.2 years ago by
Assa Yeroslaviz
★ 1.9k
121,041 results • Page
1 of 2421
Recent Votes
Comment: Addressing two nuisance factors in RNAseq
Answer: Addressing two nuisance factors in RNAseq
Answer: make a heat map with python
Answer: STAR vs. Kallisto
Answer: STAR vs. Kallisto
Comment: Addressing two nuisance factors in RNAseq
Answer: ggplot of two data set with different colors
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Recent Replies
Comment: STAR vs. Kallisto
by
dsull
★ 7.4k
On the contrary, I think the right approach is to test each tool and see where the difference arises :) -- papers would be much more inform…
Comment: STAR vs. Kallisto
by
ATpoint
87k
I use salmon-tximport/lengthScaledTPM-limma most of the time but other combinations work fine as well.
Answer: STAR vs. Kallisto
by
dsull
★ 7.4k
I use both STAR and kallisto extensively (and I help develop the latter). kallisto is nice when you care about asking the question "does…
Comment: STAR vs. Kallisto
by
gogeni5529
▴ 60
Thanks for the explanation. Do you use salmon after STAR and followed by DESeq2 to do differential expression analysis (using tximport)? Or…
Comment: Addressing two nuisance factors in RNAseq
by
ATpoint
87k
Yes. As @jaredandrews07 says.
Answer: STAR vs. Kallisto
by
ATpoint
87k
Basically, choice of tools is always a bit of arbitrary given that both tools are established and well recognized. STAR does splice-aware …
Comment: Is there a tool to obtain GO terms for thousands of genes at once?
by
Ana
▴ 10
Is there a tool to do this but with KEGG pathways instead? Thanks.
Answer: Phylogenetic Comparative Methods in R (12–16 May, Online)
by
Meeru
• 0
Thanks for the heads-up! Sounds like a great opportunity for anyone working with phylogenies and R. Definitely useful for evolutionary rese…
Comment: Is vg toolkit suitable for haplotype calling?
by
Jordan M Eizenga
▴ 700
The read alignment is a path through the graph, so in that sense, I think the read alignment might be the path you are looking for. For dow…
Answer: Biostar handbook
by
GenoMax
150k
There is no hard copy available AFAIK. After purchasing a license you get access to a PDF (in addition to the online version) that you coul…
Comment: Addressing two nuisance factors in RNAseq
by
jared.andrews07
★ 18k
Yes, that is what they're suggesting, as it is the simplest model for what you want (and makes the `RNA_extraction_day` and `library_prep_d…
Answer: pangenome - Create a diagram venn
by
mplace
▴ 40
I used supervenn, makes a nice easy to read venn alternative "https://github.com/gecko984/supervenn"
Comment: Addressing two nuisance factors in RNAseq
by
jkim
▴ 190
Thanks, ATpoint. But I'm not sure if I understand your suggestion. Are you suggesting the following design? ``` | sample_name | treatment …
Answer: Addressing two nuisance factors in RNAseq
by
ATpoint
87k
You have an extraction core? That's awesome. Anyway, why not keeping it as a single blocking factor. The samples extracted as A get preppe…
Comment: DRAGEN FILTER
by
GenoMax
150k
Equivalence of commands in the two modes is discussed in the first link above. Did you check that?
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