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116,807 results • Page
1 of 2337
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monocle 3-- Could not get node in small cluster
monocle3
10 minutes ago by
synat.keam
▴ 100
0
votes
1
reply
23
views
Correlating Bulk Differential Expression with quantitative
Expression
Differential
DESeq2
updated 49 minutes ago by
Qroid
▴ 40 • written 56 minutes ago by
Nicholas
• 0
1
vote
4
replies
232
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
2 hours ago by
heelpPlease
• 0
795
votes
167
replies
143k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.7k • written 7.4 years ago by
Istvan Albert
100k
5
votes
1
reply
74
views
TFs and Gene databases
Transcription-factor
Target
Regulatory-Networks
updated 1 hour ago by
Ram
43k • written 4 hours ago by
ijarne
• 0
0
votes
5
replies
255
views
Applying the metacell2 algorithm using python
python
single-cell
scanpy
metacell2
updated 1 hour ago by
Ram
43k • written 1 day ago by
JACKY
▴ 140
0
votes
3
replies
118
views
Filtering Multi-sample VCF file for all except one Genotype
variant
SNP
VCF
updated 1 hour ago by
Ram
43k • written 5 hours ago by
schmince
• 0
0
votes
0
replies
49
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
6 hours ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
392
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 6 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
73
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 6 hours ago by
GenoMax
142k • written 6 hours ago by
Sony
▴ 10
5
votes
5
replies
186
views
Help with running egsea()
EGSEA
19 minutes ago by
Chris
▴ 280
0
votes
1
reply
84
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 9 hours ago by
ATpoint
82k • written 9 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
153
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 6 hours ago by
i.sudbery
19k • written 9 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
102
views
student
epitranscriptomics
updated 9 hours ago by
ATpoint
82k • written 10 hours ago by
useriwa
• 0
0
votes
0
replies
61
views
Imputation of missing genotypes
panel
beagle
imputation
10 hours ago by
analyst
▴ 30
0
votes
3
replies
121
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 7 hours ago by
GenoMax
142k • written 10 hours ago by
Assa Yeroslaviz
★ 1.8k
5
votes
1
reply
94
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 10 hours ago by
dariober
14k • written 10 hours ago by
nhaus
▴ 340
1
vote
1
reply
69
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
updated 10 hours ago by
Papyrus
★ 2.9k • written 11 hours ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
193
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 11 hours ago by
Weiwen
• 0 • written 1 day ago by
MICOS
▴ 10
0
votes
0
replies
56
views
Correlation Analysis
statistics
methylation
NGS
expression
11 hours ago by
Researcher
▴ 30
1
vote
2
replies
119
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
5 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
167
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 8 hours ago by
Michael
54k • written 1 day ago by
Guillermo
• 0
1
vote
1
reply
89
views
Gene density plot
density
gene
updated 6 hours ago by
dthorbur
★ 1.9k • written 12 hours ago by
gubrins
▴ 290
1
vote
3
replies
126
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 11 hours ago by
Michael
54k • written 13 hours ago by
qwertyuiop26
• 0
0
votes
1
reply
122
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 14 hours ago by
ATpoint
82k • written 1 day ago by
MAPK2
▴ 40
0
votes
2
replies
159
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 17 hours ago by
Xiaofen
• 0 • written 19 hours ago by
toddknutson
▴ 60
0
votes
1
reply
98
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 21 hours ago by
LChart
3.9k • written 22 hours ago by
David
• 0
1
vote
2
replies
129
views
Where to get the following bed file?
WES
bed
reference
file
updated 1 day ago by
GenoMax
142k • written 1 day ago by
wyuan37
• 0
0
votes
0
replies
76
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
1 day ago by
Scott McKay
▴ 30
0
votes
0
replies
77
views
Cellphonedb results
cpdb
visulization
cellphonedb
1 day ago by
piotto
▴ 20
0
votes
0
replies
93
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
1 day ago by
belloy
• 0
0
votes
3
replies
185
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 14 hours ago by
swbarnes2
14k • written 1 day ago by
Ngrin
• 0
1
vote
6
replies
648
views
anRichment is missing
WGCNA
anRichment
updated 1 day ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
173
views
Gene ontology and homologs
gene-ontology
updated 1 day ago by
geneontologyhelp
▴ 400 • written 2 days ago by
beshka194
• 0
1
vote
2
replies
187
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 1 day ago by
zx8754
11k • written 1 day ago by
snajafy
• 0
0
votes
0
replies
84
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
0
votes
0
replies
77
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
6
replies
401
views
Question regarding WGCNA
WGCNA
Network-construction
updated 6 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
85
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
1
vote
0
replies
113
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
1 day ago by
Biostar
2.7k
0
votes
1
reply
135
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 10 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
95
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 1 day ago by
Ram
43k • written 1 day ago by
sidrah.maryam
▴ 50
0
votes
0
replies
84
views
Normalizing AMR gene count data
abundance
RGI
updated 1 day ago by
Ram
43k • written 1 day ago by
arshad1292
▴ 100
0
votes
0
replies
96
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 1 day ago by
Pierre Lindenbaum
161k • written 1 day ago by
sarumonsus
• 0
1
vote
2
replies
272
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
1 day ago by
M.
▴ 30
0
votes
0
replies
102
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
1
vote
5
replies
277
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 1 day ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
2
replies
239
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 1 day ago by
GenoMax
142k • written 2 days ago by
mropri
▴ 150
0
votes
1
reply
295
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 1 day ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
2
votes
2
replies
223
views
STRING-DB API can't find my protein but I can find it when I go to the STRING-DB website directly
STRING-DB
protein
STRING-DB-API
1 day ago by
brandon
• 0
116,807 results • Page
1 of 2337
Recent Votes
Answer: Tissue-specific DEG analysis with DEseq2
Answer: TFs and Gene databases
Answer: TFs and Gene databases
Comment: How to access TCGA samples that were treated with a specific drug?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
Answer: TFs and Gene databases
Answer: TFs and Gene databases
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Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 400
The md5 hash they refer to on line 22 (f46a7ca244afef522b22a11bd33d27b1) appears to map to a *S. aureus* strain, not *S. hominis* (you can …
Comment: Correlating Bulk Differential Expression with quantitative
by
Qroid
▴ 40
You could try including disease scale for each sample as a design factor. See the vignette here https://bioconductor.org/packages/devel/bio…
Comment: Help with generating annotation database for dog genome to use in ANNOVAR for v
by
sainavyav22
• 0
Hello, Thanks for the reply. I could only see the refMrna.fa file in the link you provided. Where can I get the refGene.txt file. Thanks fo…
Answer: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
After thoroughly reviewing all the documents again, I've identified the root cause of my initial issue: the failure to detect essential gen…
Comment: Understanding STAR output (Aligned.out.sam file)
by
heelpPlease
• 0
Thank you! Now that I understand that there is a difference between read and fragment, I could actually find a lot of helpful information..…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Thanks again. Hmm...this makes me suspicious of whether this normalization is actually possible. In case you'd like to take a look, [here]…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Jeremy Leipzig
22k
The seven genotypes being 58025AA, 58025AG, 58051TT, 58051TC, 58051CC, 58057TT, 58057TC
Answer: TFs and Gene databases
by
jared.andrews07
★ 16k
See [TFlink](https://tflink.net/), [KnockTF2](https://bio.liclab.net/KnockTFv2/index.php), [TFBSDB](https://tfbsdb.systemsbiology.net/), an…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
GenoMax
142k
> Seven genotpyes have been sampled and all variants, which belong to one of those genotpyes are to be "erased" (or every other variant exc…
Comment: Filtering Multi-sample VCF file for all except one Genotype
by
Pierre Lindenbaum
161k
> , filter a multisample VCF file for all genotypes except one of them filter for what ?
Answer: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
I had hoped things like [this Jupyter notebook for the rabbit data analysis](https://nbviewer.org/github/tanaylab/rabembflow/blob/master/2-…
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
please provide the design matrix mean the metadata of the model fit2 which is there in the code . i guess other users can help
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
The repo does not provide any valuable information unfortunately. The Metacell algorithm they provide in the vignette is missing the metagr…
Comment: Repeated testing/data mining in RNA Seq
by
robert.flynn.21
• 0
Thanks! I'll give it a go.
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
Yes, they are very clear about this. The page about the Vignettes says: >"They are not meant as a comprehensive documentation of all the fe…
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