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13,539 results • Page
1 of 271
Sort: Rank
Rank
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Votes
Replies
1
vote
2
replies
26
views
Help with running egsea()
EGSEA
3 minutes ago by
Chris
▴ 260
0
votes
1
reply
25
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 1 hour ago by
ATpoint
82k • written 1 hour ago by
ahmad.sajad4541
• 0
0
votes
0
replies
16
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
1 hour ago by
Assa Yeroslaviz
★ 1.8k
0
votes
1
reply
38
views
student
epitranscriptomics
updated 1 hour ago by
ATpoint
82k • written 2 hours ago by
useriwa
• 0
0
votes
0
replies
28
views
Imputation of missing genotypes
panel
beagle
imputation
2 hours ago by
analyst
▴ 30
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
0
votes
1
reply
34
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 45 minutes ago by
GenoMax
142k • written 2 hours ago by
Assa Yeroslaviz
★ 1.8k
3
votes
1
reply
45
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 2 hours ago by
dariober
14k • written 2 hours ago by
nhaus
▴ 330
1
vote
1
reply
40
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
updated 2 hours ago by
Papyrus
★ 2.9k • written 2 hours ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
169
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 2 hours ago by
Weiwen
• 0 • written 1 day ago by
MICOS
▴ 10
0
votes
0
replies
27
views
Correlation Analysis
statistics
methylation
NGS
expression
3 hours ago by
Researcher
▴ 30
0
votes
1
reply
46
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
updated 50 minutes ago by
ATpoint
82k • written 3 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
137
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 40 minutes ago by
Michael
54k • written 16 hours ago by
Guillermo
• 0
0
votes
0
replies
36
views
Gene density plot
density
gene
4 hours ago by
gubrins
▴ 290
0
votes
3
replies
163
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
updated 4 hours ago by
i.sudbery
19k • written 13 hours ago by
heelpPlease
• 0
1
vote
3
replies
99
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 3 hours ago by
Michael
54k • written 5 hours ago by
qwertyuiop26
• 0
0
votes
1
reply
110
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 6 hours ago by
ATpoint
82k • written 22 hours ago by
MAPK2
▴ 40
0
votes
1
reply
107
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 9 hours ago by
Xiaofen
• 0 • written 11 hours ago by
toddknutson
▴ 60
0
votes
1
reply
85
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 13 hours ago by
LChart
3.9k • written 13 hours ago by
David
• 0
1
vote
2
replies
116
views
Where to get the following bed file?
WES
bed
reference
file
updated 15 hours ago by
GenoMax
142k • written 16 hours ago by
wyuan37
• 0
0
votes
0
replies
63
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
16 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
64
views
Cellphonedb results
cpdb
visulization
cellphonedb
16 hours ago by
piotto
▴ 20
0
votes
0
replies
80
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
17 hours ago by
belloy
• 0
0
votes
3
replies
172
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 6 hours ago by
swbarnes2
14k • written 18 hours ago by
Ngrin
• 0
0
votes
2
replies
131
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
1 hour ago by
JACKY
▴ 140
1
vote
6
replies
634
views
anRichment is missing
WGCNA
anRichment
updated 19 hours ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
163
views
Gene ontology and homologs
gene-ontology
updated 20 hours ago by
geneontologyhelp
▴ 400 • written 1 day ago by
beshka194
• 0
1
vote
2
replies
174
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 18 hours ago by
zx8754
11k • written 1 day ago by
snajafy
• 0
0
votes
0
replies
74
views
Cox Model with interaction item interpretation
Cox
22 hours ago by
Bine
▴ 60
0
votes
0
replies
65
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
22 hours ago by
Javier
• 0
1
vote
4
replies
327
views
Question regarding WGCNA
WGCNA
Network-construction
updated 20 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
73
views
vdjtools
vdjtools
23 hours ago by
yueli7
▴ 250
1
vote
0
replies
102
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
23 hours ago by
Biostar
2.7k
0
votes
1
reply
120
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 2 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
85
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
73
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
84
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
0
votes
2
replies
259
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
18 hours ago by
M.
▴ 30
0
votes
0
replies
92
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
1
vote
5
replies
266
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
198
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 1 day ago by
mropri
▴ 150
0
votes
1
reply
284
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
211
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
0
votes
0
replies
107
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
1 day ago by
KHURRAM SHAHZAD
• 0
1
vote
5
replies
340
views
install package: package ‘gmwm’ 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
0
replies
104
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
1 day ago by
Christopher
• 0
4
votes
1
reply
217
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 1 day ago by
zx8754
11k • written 2 days ago by
Jautis
▴ 560
2
votes
2
replies
303
views
Association study using SNP data
Association
Allele
Parentage
SNP
1 day ago by
drajangirija
• 0
0
votes
0
replies
100
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
2 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
112
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
2 days ago by
DGTool
• 0
13,539 results • Page
1 of 271
Recent Votes
Comment: Help with running egsea()
Comment: Question regarding WGCNA
Comment: Bacterial plasmid analysis
Comment: Bacterial plasmid analysis
The Biostar Herald for Monday, May 06, 2024
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
Answer: Is therer any suggestions on mapping rate of WGBS data?
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Recent Awards •
All
Popular Question
to
Papyrus
★ 2.9k
Popular Question
to
hkarakurt
▴ 180
Commentator
to
GenoMax
142k
Popular Question
to
anasjamshed
▴ 120
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161k
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Omics data mining
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Recent Replies
Comment: Help with running egsea()
by
Chris
▴ 260
Thanks 1769mkc! I tried this tool. Gene expression of 2 groups is just slightly different (not hundred of differential express genes). The …
Comment: Help with running egsea()
by
1769mkc
★ 1.2k
https://metascape.org/ this is one of the ways to make life easier if you have the genes already from the differential list
Comment: RNA editing sites based on DNA seq and RNA seq
by
Ahiad Chen Zion
• 0
In those unaligned reads, I am looking for hyper-editing. But the alignment should be much higher
Comment: Bacterial plasmid analysis
by
GenoMax
142k
Once you have some of these basic issues sorted out you can create a `tools` post describing `pling`.
Comment: Bacterial plasmid analysis
by
Daria
▴ 30
Hi, you need to run it with `PYTHONPATH=<pling_path>` in front of the command (a bit clunky, I know -- will likely be fixed in the next ver…
Comment: trying to count a pattern in my fastq file using bbduk
by
GenoMax
142k
I don't think you can use N's in `literal=` since the match is literal as the option says. Depending where in the read this pattern is you …
Comment: Repeated testing/data mining in RNA Seq
by
ATpoint
82k
> As such, I am wondering what the protocol is here? My personal suggestion is to just do it and see what comes out. Multiple comparisons …
Comment: Applying the metacell2 algorithm using python
by
JACKY
▴ 140
I've followed this [vignette][1] [1]: https://tanaylab.github.io/metacells-vignettes/iterative.html Which is the only pipeline that d…
Comment: Bacterial plasmid analysis
by
GenoMax
142k
https://www.biostars.org/u/98332/ : This may be best posted as a new question since you are now running into a problem with tool usage.
Comment: Differentail gene expression results
by
ATpoint
82k
What is your question? See https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html which covers most relevan…
Comment: HCL database download
by
GenoMax
142k
Please post your solution as an answer.
Comment: student
by
ATpoint
82k
Please --- https://www.biostars.org/p/357878/ https://www.biostars.org/p/75548/ [Ten Simple Rules for Getting Help from Online Scientifi…
Comment: High Malat-1 expression in single cell data
by
carolofharvest
▴ 30
If rRNA genes have been mistakenly assigned to these genes, could it be expected that the percentage of ribosomal genes(rpl,rps) would be …
Comment: removeBatchEffect explained using base R linear models
by
dariober
14k
(+1) *"implementing" the method just using base R linear models.*: I find implementing from basic starting point to be one of the best, if …
Answer: Is therer any suggestions on mapping rate of WGBS data?
by
Papyrus
★ 2.9k
Mapping rate for bisulfite data is typically worse because of reduced complexity of the sequences. The efficiency will depend on your read …
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