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170 results • Page
1 of 4
Sort: Rank
Rank
Views
Votes
Replies
1
vote
5
replies
199
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
38 minutes ago by
heelpPlease
• 0
3
votes
1
reply
44
views
TFs and Gene databases
factor
Target
Regulatory
Transcription
Networks
updated 1 hour ago by
jared.andrews07
★ 16k • written 2 hours ago by
ijarne
• 0
0
votes
5
replies
233
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
updated 2 hours ago by
Wayne
★ 2.0k • written 1 day ago by
JACKY
▴ 140
0
votes
3
replies
80
views
Filtering Multi-sample VCF file for all except one Genotype
SNP
genotype
filter
variant
VCF
updated 1 hour ago by
Jeremy Leipzig
22k • written 3 hours ago by
schmince
• 0
0
votes
0
replies
41
views
News:
Online course. -Time series analysis and Forecasting in R
Time-Series
Forecasting
R
Stastics
4 hours ago by
carlopecoraro2
★ 2.5k
0
votes
2
replies
383
views
HLA-HD tool for genomic imputation
genomics
imputation
bash
updated 4 hours ago by
Javier
• 0 • written 3 months ago by
fra.r.silvestro
▴ 10
0
votes
1
reply
64
views
ERROR: Duplicate entry "..." in sam header; samtools view: failed to add PG line to the header
sort.
SAMtools.
BAM.
SAM.
updated 5 hours ago by
GenoMax
142k • written 5 hours ago by
Sony
▴ 10
5
votes
5
replies
166
views
Help with running egsea()
EGSEA
2 hours ago by
Chris
▴ 280
0
votes
1
reply
79
views
Differentail gene expression results
differential
expression
gene
rna-seq
Deseq2
updated 7 hours ago by
ATpoint
82k • written 7 hours ago by
ahmad.sajad4541
• 0
1
vote
5
replies
142
views
UMI-Tools knee-method has great influence on the results of white list
single-cell
whitelist
UMI
RNA
UMI-Tools
updated 5 hours ago by
i.sudbery
19k • written 8 hours ago by
Assa Yeroslaviz
★ 1.8k
1
vote
1
reply
96
views
student
epitranscriptomics
updated 8 hours ago by
ATpoint
82k • written 8 hours ago by
useriwa
• 0
0
votes
0
replies
55
views
Imputation of missing genotypes
panel
beagle
imputation
8 hours ago by
analyst
▴ 30
0
votes
3
replies
115
views
trying to count a pattern in my fastq file using bbduk
java
bbduk
bbmap
fastq
updated 5 hours ago by
GenoMax
142k • written 9 hours ago by
Assa Yeroslaviz
★ 1.8k
5
votes
1
reply
87
views
Tutorial:
removeBatchEffect explained using base R linear models
limma
effects
batch
removebatcheffects
updated 8 hours ago by
dariober
14k • written 9 hours ago by
nhaus
▴ 340
1
vote
1
reply
64
views
Is therer any suggestions on mapping rate of WGBS data?
mapping
read
alignment
WGBS
updated 8 hours ago by
Papyrus
★ 2.9k • written 9 hours ago by
Zeng Jingyu
▴ 60
1
vote
2
replies
190
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 9 hours ago by
Weiwen
• 0 • written 1 day ago by
MICOS
▴ 10
0
votes
0
replies
50
views
Correlation Analysis
statistics
methylation
NGS
expression
9 hours ago by
Researcher
▴ 30
1
vote
2
replies
105
views
Repeated testing/data mining in RNA Seq
repeated
RNA-Seq
mining
testing
data
3 hours ago by
robert.flynn.21
• 0
1
vote
1
reply
163
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
updated 7 hours ago by
Michael
54k • written 22 hours ago by
Guillermo
• 0
1
vote
1
reply
78
views
Gene density plot
density
gene
updated 4 hours ago by
dthorbur
★ 1.9k • written 10 hours ago by
gubrins
▴ 290
1
vote
3
replies
121
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
updated 10 hours ago by
Michael
54k • written 11 hours ago by
qwertyuiop26
• 0
0
votes
1
reply
120
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 12 hours ago by
ATpoint
82k • written 1 day ago by
MAPK2
▴ 40
0
votes
2
replies
149
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 15 hours ago by
Xiaofen
• 0 • written 17 hours ago by
toddknutson
▴ 60
0
votes
1
reply
96
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 19 hours ago by
LChart
3.9k • written 20 hours ago by
David
• 0
1
vote
2
replies
127
views
Where to get the following bed file?
WES
bed
reference
file
updated 22 hours ago by
GenoMax
142k • written 22 hours ago by
wyuan37
• 0
0
votes
0
replies
73
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
23 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
74
views
Cellphonedb results
cpdb
visulization
cellphonedb
23 hours ago by
piotto
▴ 20
0
votes
0
replies
90
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
23 hours ago by
belloy
• 0
0
votes
3
replies
183
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 13 hours ago by
swbarnes2
14k • written 1 day ago by
Ngrin
• 0
1
vote
6
replies
644
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
171
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
183
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
82
views
Cox Model with interaction item interpretation
Cox
1 day ago by
Bine
▴ 60
0
votes
0
replies
75
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
1 day ago by
Javier
• 0
1
vote
6
replies
393
views
Question regarding WGCNA
WGCNA
Network-construction
updated 4 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
83
views
vdjtools
vdjtools
1 day ago by
yueli7
▴ 250
1
vote
0
replies
111
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
1 day ago by
Biostar
2.7k
0
votes
1
reply
131
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 8 hours ago by
andres.firrincieli
3.6k • written 1 day ago by
Antonio
• 0
0
votes
0
replies
92
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
81
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
92
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
268
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
1 day ago by
M.
▴ 30
0
votes
0
replies
99
views
How to implement an IGV to streamlit app?
python
streamlit
igv
1 day ago by
avigail.shnaider
• 0
1
vote
5
replies
275
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
233
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
293
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
221
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
115
views
Mitogenomes gap closure and making circular genome
gapclosure
Mitogenomes
validation
circulargenome
2 days ago by
KHURRAM SHAHZAD
• 0
1
vote
5
replies
348
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 1 day ago by
Ram
43k • written 2 days ago by
snajafy
• 0
0
votes
0
replies
110
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
2 days ago by
Christopher
• 0
170 results • Page
1 of 4
Recent Votes
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
Answer: TFs and Gene databases
Answer: Understanding STAR output (Aligned.out.sam file)
Comment: High Malat-1 expression in single cell data
Comment: removeBatchEffect explained using base R linear models
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Recent Replies
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…
Comment: Gene density plot
by
dthorbur
★ 1.9k
This sounds like it would be a simple task in either python or R. Read data in, potentially with a library like `data.table` in `R`, depend…
Answer: HLA-HD tool for genomic imputation
by
Javier
• 0
Hi, I just solved the same error. In my case, it was because I misunderstood the instructions. hlahd.sh -t 4 *-f ~/hlahd.1.7.0/fr…
Comment: Question regarding WGCNA
by
andres.firrincieli
3.6k
Ok, then. You likely have a scale free topology that look like this: [link][1] In this situation you should pick the power value with an …
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