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44 results • Page
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12
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Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
updated just now by
LChart
3.9k • written 45 minutes ago by
David
• 0
0
votes
0
replies
6
views
Understanding STAR output (Aligned.out.sam file)
STAR
paired-end
read
7 minutes ago by
heelpPlease
• 0
1
vote
2
replies
63
views
Where to get the following bed file?
WES
bed
reference
file
updated 2 hours ago by
GenoMax
142k • written 3 hours ago by
wyuan37
• 0
0
votes
0
replies
38
views
Tool:
Converting Nebula Genomics Data to 23andMe Format
23andMe
Nebula
2 hours ago by
Guillermo
• 0
0
votes
0
replies
37
views
Get Paired TCRa/b from MIXCR
python
r
mixcr
tcr_seq
3 hours ago by
Scott McKay
▴ 30
0
votes
0
replies
37
views
Cellphonedb results
cpdb
visulization
cellphonedb
3 hours ago by
piotto
▴ 20
0
votes
0
replies
43
views
Job:
Post-doctoral Position in Alzheimer’s Disease Genetics, ‘Omics, and Biomarkers
Genomics
Alzheimer
multiomics
neuroimaging
3 hours ago by
belloy
• 0
0
votes
2
replies
99
views
How to compute TPM normalized values for TCGA miRNA data?
TCGA
normalization
TPM
miRNA
3 hours ago by
Ngrin
• 0
0
votes
1
reply
83
views
Applying the metacell2 algorithm using python
single-cell
scanpy
cells
meta
python
updated 4 hours ago by
Wayne
★ 2.0k • written 6 hours ago by
JACKY
▴ 140
1
vote
6
replies
586
views
anRichment is missing
WGCNA
anRichment
updated 6 hours ago by
GenoMax
142k • written 5 months ago by
michael.flower.14
▴ 180
1
vote
1
reply
137
views
Gene ontology and homologs
gene-ontology
updated 7 hours ago by
geneontologyhelp
▴ 400 • written 1 day ago by
beshka194
• 0
1
vote
2
replies
150
views
error in R code: Error in fit_avlr(...), : wn incorrectly formatted
R
updated 5 hours ago by
zx8754
11k • written 13 hours ago by
snajafy
• 0
0
votes
0
replies
52
views
Cox Model with interaction item interpretation
Cox
9 hours ago by
Bine
▴ 60
0
votes
0
replies
52
views
What is the proper way to identify the cell types of scRNAseq cluster?
scRNAseq
9 hours ago by
MAPK2
▴ 40
0
votes
0
replies
44
views
how to downlad slices of CRAM fro ICGC ARGO
icgc
samtools
cram
9 hours ago by
Javier
• 0
0
votes
4
replies
298
views
Question regarding WGCNA
WGCNA
Network-construction
updated 7 hours ago by
andres.firrincieli
3.6k • written 3 days ago by
deepak
• 0
0
votes
0
replies
52
views
vdjtools
vdjtools
10 hours ago by
yueli7
▴ 250
0
votes
0
replies
70
views
Herald:
The Biostar Herald for Monday, May 06, 2024
herald
10 hours ago by
Biostar
2.7k
0
votes
1
reply
92
views
16S rRNA microbiome differential abundance analysis with DESeq2 finds same microbial Genus in both groups.
microbiome
16S
DESeq2
updated 7 hours ago by
andres.firrincieli
3.6k • written 11 hours ago by
Antonio
• 0
0
votes
0
replies
64
views
Error while loading model of Spatial data deconvolution using cell2location
Python
cell2location
updated 12 hours ago by
Ram
43k • written 12 hours ago by
sidrah.maryam
▴ 50
0
votes
0
replies
50
views
Normalizing AMR gene count data
abundance
RGI
updated 11 hours ago by
Ram
43k • written 12 hours ago by
arshad1292
▴ 100
0
votes
0
replies
72
views
News:
We created a Bioinformatics Competition for Spatial Transcriptomics: MICOS-EU
cell-clustering
Spatial-transcriptomics
updated 11 hours ago by
Ram
43k • written 13 hours ago by
MICOS
• 0
0
votes
0
replies
56
views
Help with VG Toolkit: VCF Output is Empty
vg
updated 15 hours ago by
Pierre Lindenbaum
161k • written 15 hours ago by
sarumonsus
• 0
0
votes
2
replies
242
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
5 hours ago by
M.
▴ 30
0
votes
0
replies
73
views
How to implement an IGV to streamlit app?
python
streamlit
igv
16 hours ago by
avigail.shnaider
• 0
1
vote
5
replies
247
views
install.packages("imudata") - package ‘imudata’ is not available for this version of R
r
updated 11 hours ago by
Ram
43k • written 17 hours ago by
snajafy
• 0
0
votes
2
replies
168
views
Error in checkFullRank(modelMatrix) : the model matrix is not full rank, so the model cannot be fit as specified.
DESeq2
updated 12 hours ago by
GenoMax
142k • written 1 day ago by
mropri
▴ 150
0
votes
1
reply
267
views
DMRcate ranges liftover hg19 to hg38
DMRcate
Liftover
DMR
Methylation
annotation
updated 23 hours ago by
aaron.stevens
• 0 • written 12 weeks ago by
sativus
▴ 20
1
vote
5
replies
316
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 10 hours ago by
Ram
43k • written 1 day ago by
snajafy
• 0
4
votes
1
reply
198
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 16 hours ago by
zx8754
11k • written 2 days ago by
Jautis
▴ 560
0
votes
1
reply
138
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 4 hours ago by
bk11
★ 2.4k • written 1 day ago by
Yoosef
▴ 60
3
votes
4
replies
374
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 2 hours ago by
Gordon Smyth
★ 7.1k • written 3 days ago by
SHN
▴ 40
0
votes
1
reply
236
views
creating batch colum for batch correction
batch-correction
combat
14 hours ago by
Expert
▴ 10
0
votes
2
replies
218
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
8 hours ago by
kalavattam
▴ 190
1
vote
0
replies
142
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 16 hours ago by
zx8754
11k • written 3 days ago by
Emilie
▴ 10
10
votes
10
replies
615
views
High Malat-1 expression in single cell data
single-cell
updated 12 hours ago by
t.montserrat.ayuso
▴ 10 • written 7 days ago by
carolofharvest
▴ 30
0
votes
5
replies
337
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 3 hours ago by
Chris Dean
▴ 390 • written 4 days ago by
sovrappensiero
▴ 90
2
votes
8
replies
463
views
How to access TCGA samples that were treated with a specific drug?
TCGA
RNA-seq
5 hours ago by
Qroid
▴ 40
1
vote
3
replies
280
views
ERROR When Using Ensembl Plants Biomart Wget API
biomart
plant
ensembl
19 hours ago by
Dora
▴ 10
2
votes
2
replies
183
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
updated 11 hours ago by
GenoMax
142k • written 6 days ago by
Adyasha
• 0
0
votes
0
replies
176
views
CellPhoneDB results
cellphonedb
cpdb
cell_surface_proteins
updated 3 hours ago by
GenoMax
142k • written 10 weeks ago by
piotto
▴ 20
1
vote
10
replies
838
views
error to run rnammer
phylogenomics
rRNA_extraction
rnammer
updated 17 hours ago by
antonio.spl
• 0 • written 3 months ago by
microorganism_001
▴ 30
1
vote
11
replies
5.5k
views
Truncated Bam Error
R
next-gen
sequencing
software error
updated 20 hours ago by
guanghao
• 0 • written 6.1 years ago by
vivekruhela
▴ 20
4
votes
6
replies
3.8k
views
How to interpret DEXseq results in therms of significance
DEXseq
RNA-Seq
exon
updated 10 hours ago by
Sara
▴ 30 • written 6.7 years ago by
Lila M
★ 1.2k
44 results • Page
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Comment: Which hg38 file?
Answer: Which hg38 file?
Answer: Where to get the following bed file?
How to save GRanges object to csv file
Answer: How to get proteins from GFF file resulted from MAKER annotation
Answer: Gene ontology and homologs
Comment: anRichment is missing
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Recent Replies
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 S…
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…
Answer: Where to get the following bed file?
by
LChart
3.9k
UCSC maintains a list of exome probe sets and targets. You could check there: https://hgdownload.soe.ucsc.edu/gbdb/hg19/exomeProbesets/
Comment: How to compute TPM normalized values for TCGA miRNA data?
by
Ngrin
• 0
Yes, I found some similar ideas on biostar repository. So you think the authors have done something wrong? And I should only consider CPM?
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
It is difficult to answer how they were able to identify *S. hominis* without seeing the code or paper. To address your second question, i…
Comment: Problem with Seurat package in PercentageFeatureSet function
by
bk11
★ 2.4k
Did you check where the `features.tsv.gz` file had Gene IDs or Ensembl IDs?
Answer: How to compute TPM normalized values for TCGA miRNA data?
by
dsull
★ 6.0k
TPM is irrelevant for miRNA-seq; CPM works fine. TPM tries to adjust for length effects by dividing by gene length (e.g. reducing the im…
Comment: Applying the metacell2 algorithm using python
by
Wayne
★ 2.0k
"I'm also unsure what qualifies as a lateral gene." The [README where you reference](https://metacells.readthedocs.io/en/latest/readme.htm…
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
sovrappensiero
▴ 90
Ah, yes this makes sense! I knew this was an issue with, say, using kraken2 on shotgun metagenomic reads, but I don't have a lot of experi…
Comment: How to access TCGA samples that were treated with a specific drug?
by
Qroid
▴ 40
Thank you. Maybe it's best to confirm with the authors about how they're getting responder/non-responder labels. I'll do that now.
Comment: Spike-in control found in raw reads (16S amplicon seq) but not picked up by DADA
by
Chris Dean
▴ 390
If you sequenced a short hypervariable region, most of your sequence reads will not be able to be assigned to the species level. One possi…
Comment: anRichment is missing
by
GenoMax
142k
Consider emailing Dr. Horvath about this. Until enough people make him aware of this issue WGCNA "problem" is unlikely to get fixed.
Comment: anRichment is missing
by
Tatyana
• 0
Unfortunately, there are only tutorials and codes for tutorials for WGCNA, not installation files for any their packages... :(
Comment: anRichment is missing
by
GenoMax
142k
See this link for the WGCNA documentation and code from Peter Langfelder : https://bioinformatics.stackexchange.com/questions/21885/where-t…
Comment: anRichment is missing
by
Tatyana
• 0
The problem is back, Horwath's lab web is down again. Is it possible to get anRichment istallation file somewhere? (The greater problem is …
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