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43 results • Page
1 of 1
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0
votes
0
replies
5
views
Gene density plot
density
gene
2 minutes ago by
gubrins
▴ 290
0
votes
3
replies
118
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
updated 51 minutes ago by
i.sudbery
19k • written 9 hours ago by
heelpPlease
• 0
0
votes
2
replies
28
views
Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, Complexity, and Use Cases
fmindex
bwt
just now by
qwertyuiop26
• 0
0
votes
1
reply
92
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
updated 2 hours ago by
ATpoint
82k • written 18 hours ago by
MAPK2
▴ 40
0
votes
1
reply
84
views
Job:
Bioinformatics Analyst - Laboratory Medicine and Pathology
job
updated 5 hours ago by
Xiaofen
• 0 • written 7 hours ago by
toddknutson
▴ 60
0
votes
1
reply
75
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated 9 hours ago by
LChart
3.9k • written 9 hours ago by
David
• 0
1
vote
2
replies
107
views
Where to get the following bed file?
WES
bed
reference
file
updated 12 hours ago by
GenoMax
142k • written 12 hours ago by
wyuan37
• 0
0
votes
0
replies
90
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
11 hours ago by
Guillermo
• 0
0
votes
0
replies
59
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
12 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
58
views
Cellphonedb results
cpdb
visulization
cellphonedb
12 hours ago by
piotto
▴ 20
0
votes
0
replies
70
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
12 hours ago by
belloy
• 0
0
votes
3
replies
154
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
updated 2 hours ago by
swbarnes2
14k • written 14 hours ago by
Ngrin
• 0
0
votes
1
reply
116
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
updated 13 hours ago by
Wayne
★ 2.0k • written 15 hours ago by
JACKY
▴ 140
1
vote
6
replies
630
views
anRichment is missing
WGCNA
anRichment
updated 15 hours ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
159
views
Gene ontology and homologs
gene-ontology
updated 16 hours ago by
geneontologyhelp
▴ 400 • written 1 day ago by
beshka194
• 0
1
vote
2
replies
169
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 14 hours ago by
zx8754
11k • written 22 hours ago by
snajafy
• 0
0
votes
0
replies
69
views
Cox Model with interaction item interpretation
Cox
18 hours ago by
Bine
▴ 60
0
votes
0
replies
61
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
18 hours ago by
Javier
• 0
0
votes
4
replies
317
views
Question regarding WGCNA
WGCNA
Network-construction
updated 16 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
69
views
vdjtools
vdjtools
19 hours ago by
yueli7
▴ 250
0
votes
0
replies
92
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
19 hours ago by
Biostar
2.7k
0
votes
1
reply
114
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 16 hours ago by
andres.firrincieli
3.6k • written 20 hours ago by
Antonio
• 0
0
votes
0
replies
80
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 21 hours ago by
Ram
43k • written 21 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
67
views
Normalizing AMR gene count data
abundance
RGI
updated 21 hours ago by
Ram
43k • written 21 hours ago by
arshad1292
▴ 100
0
votes
1
reply
122
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
6 hours ago by
MICOS
• 0
0
votes
2
replies
255
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
14 hours ago by
M.
▴ 30
1
vote
5
replies
262
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 21 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
2
replies
185
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 21 hours ago by
GenoMax
142k • written 1 day ago by
mropri
▴ 150
1
vote
5
replies
335
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 20 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
0
votes
1
reply
165
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 13 hours ago by
bk11
★ 2.4k • written 2 days ago by
Yoosef
▴ 60
3
votes
4
replies
394
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 11 hours ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
SHN
▴ 40
0
votes
1
reply
250
views
creating batch colum for batch correction
batch-correction
combat
23 hours ago by
Expert
▴ 10
0
votes
3
replies
242
views
HCL database download
database
HCL
human
3 hours ago by
sooni
▴ 20
0
votes
2
replies
222
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
17 hours ago by
kalavattam
▴ 190
11
votes
10
replies
622
views
High Malat-1 expression in single cell data
single-cell
updated 22 hours ago by
t.montserrat.ayuso
▴ 20 • written 7 days ago by
carolofharvest
▴ 30
0
votes
5
replies
379
views
Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA2 - where to go from here?
nf-core
16S
amplicon
dada2
ampliseq
updated 12 hours ago by
Chris Dean
▴ 390 • written 4 days ago by
sovrappensiero
▴ 90
2
votes
8
replies
483
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
14 hours ago by
Qroid
▴ 40
9
votes
11
replies
520
views
6 follow
Bacterial plasmid analysis
bacteria
plasmid
wgs
hybridassembly
sequencing
10 minutes ago by
nicole.kavanagh
• 0
3
votes
3
replies
211
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 hours ago by
Adyasha
• 0
0
votes
0
replies
177
views
CellPhoneDB results
cellphonedb
cpdb
cell_surface_proteins
updated 12 hours ago by
GenoMax
142k • written 10 weeks ago by
piotto
▴ 20
2
votes
4
replies
709
views
Count all variants from vcf file
variants
vcf
Count
updated 54 minutes ago by
Pierre Lindenbaum
161k • written 20 months ago by
t.ali
• 0
10
votes
16
replies
17k
views
7 follow
How Can I Count Snps In My Final Vcf Files
SNP
updated 51 minutes ago by
Pierre Lindenbaum
161k • written 5.7 years ago by
mostafarafiepour
▴ 180
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 19 hours ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
43 results • Page
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Recent Votes
A: Sjdboverhang Option In Star
Comment: High Malat-1 expression in single cell data
Comment: Gene Specific coverage from WGS data
Answer: ATAC-Seq and RPKM
Answer: MSA and distance matrix in R
Comment: MSA and distance matrix in R
Comment: Which hg38 file?
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Matthias Zepper
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Recent Replies
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
qwertyuiop26
• 0
I'm sorry for any confusion or inconvenience. I'm seeking guidance on which search algorithms are used in the FM-index. I've done extensive…
Comment: Bacterial plasmid analysis
by
nicole.kavanagh
• 0
Hi Daria, I have downloaded pling and the other dependencies as recommended on your github page. I have tried to run the tool a few times …
Answer: Understanding STAR output (Aligned.out.sam file)
by
i.sudbery
19k
The insert size is measured from outermost edge of this read, to the outer most edge of its mate. Like, literally, start_second - start_fir…
Comment: Comparative Analysis of Algorithms for Implementing the FM-Index: Correctness, C
by
Michael
54k
So this is your exam question or assignment? Please understand that posting this here is not doing anyone any good. You are supposed to lea…
Answer: What is the proper way to identify the cell types of scRNAseq cluster?
by
ATpoint
82k
I will say that the proper way is the one that confidently identifies your celltypes. > optimal number of marker genes to consider. T…
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
swbarnes2
14k
When everything is the same size, correcting for size is pointless. It doesn't change the numbers much at all.
Comment: Understanding STAR output (Aligned.out.sam file)
by
swbarnes2
14k
What do the alignments look like in IGV?
Comment: HCL database download
by
sooni
▴ 20
I solved the problem! Thanks!
Comment: Gene Specific coverage from WGS data
by
Adyasha
• 0
Thank you, here I am giving you some example , suppose I have bam files . 1.bam 2.bam 3.bam 4.bam now I want to see Spike gene coverage in …
Answer: Bioinformatics Analyst - Laboratory Medicine and Pathology
by
Xiaofen
• 0
I'm having a problem and I can't find the button to post, how do you post?
Comment: We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
by
MICOS
• 0
Contest question details: **To effectively address the accuracy and efficiency issues of clustering algorithms used for spatial transcript…
Comment: HCL database download
by
sooni
▴ 20
I would like to download top markers for each subpopulation data. Is there no way? It seems different from the DGE data.
Comment: Understanding STAR output (Aligned.out.sam file)
by
GenoMax
142k
Refer to SAM alignment format: https://samtools.github.io/hts-specs/SAMv1.pdf Check section 1.4.
Answer: Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genom
by
LChart
3.9k
Step 1: Go to TCGA in the GDC and open the Cohort Builder https://portal.gdc.cancer.gov/analysis_page?app=CohortBuilder&tab=general Step …
Comment: Where to get the following bed file?
by
GenoMax
142k
SeqCap kits are discontinued. If you don't find the said file your will need to email Roche Support per this page: https://sequencing.roche…
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