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1,000 results • Page
6 of 20
Sort: Rank
Rank
Views
Votes
Replies
3
votes
6
replies
484
views
install package: package ‘gmwm’ is not available for this version of R
r
updated 3 days ago by
Pine
▴ 20 • written 11 days ago by
snajafy
• 0
0
votes
0
replies
122
views
Looking for phytopathogenic, Nitrogen-Fixing, and Growth-Promoting databases for Metagenomic Analysis
Bacteria
Metagenomics
Database
11 days ago by
Christopher
• 0
4
votes
1
reply
253
views
LD-prune variants while maintaining a list of SNPs
snp
vcf
plink
filtering
independent
updated 10 days ago by
zx8754
11k • written 11 days ago by
Jautis
▴ 560
2
votes
2
replies
347
views
Association study using SNP data
Association
Allele
Parentage
SNP
11 days ago by
drajangirija
• 0
0
votes
0
replies
120
views
News:
Online course: Bioinformatic analysis of transposable elements
GenomeAssembly
Transcriptomics
TransposableElements
ManualCuration
11 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
124
views
Clarification on StringTie's `--merge` parameters
stringtie
stringtie-merge
11 days ago by
DGTool
▴ 20
2
votes
3
replies
331
views
Problem with Seurat package in PercentageFeatureSet function
cell
single
updated 6 days ago by
bk11
★ 2.4k • written 11 days ago by
Yoosef
▴ 60
0
votes
1
reply
652
views
Job:
Seeking Bioinformatics/Drug Design Opportunities - PhD in Pharmacology with Experience in RNA-seq, CADD & Deep Learning Molecular Generation
search
job
updated 11 days ago by
GenoMax
142k • written 11 days ago by
tulip
• 0
3
votes
4
replies
452
views
Design matrix Differential expression analysis
RNA-seq
Differential-expression
updated 9 days ago by
Gordon Smyth
★ 7.2k • written 12 days ago by
SHN
▴ 40
4
votes
2
replies
274
views
GRCh38.gmap file
gnomix
gmap
11 days ago by
lorena9132
▴ 10
2
votes
3
replies
841
views
Issues with Mixture file when using CIBERSORTx
Deconvolution
CIBERSORTx
updated 12 days ago by
vjanve
• 0 • written 7 months ago by
mateomejias
• 0
0
votes
1
reply
274
views
creating batch colum for batch correction
batch-correction
combat
10 days ago by
Expert
▴ 10
1
vote
4
replies
387
views
Segmentation error while using a tool
smalt
updated 12 days ago by
Mensur Dlakic
★ 27k • written 12 days ago by
Ruqaiya
• 0
0
votes
1
reply
236
views
Help with DGEList function
DGEList
R
updated 10 days ago by
marco.barr
▴ 120 • written 12 days ago by
Natali
• 0
0
votes
0
replies
166
views
Homer motif analysis
Homer
12 days ago by
daffodil
▴ 10
1
vote
2
replies
1.2k
views
News:
The GDC Legacy Archive is retiring soon.
genomic-data-commons
tcga
gdc
11 days ago by
Zhenyu Zhang
★ 1.2k
2
votes
1
reply
329
views
Force PLINK2 to neglect chrX as the sex chromosome
PLINK2
updated 12 days ago by
chrchang523
10k • written 16 days ago by
8armed
▴ 10
0
votes
5
replies
377
views
Easy way to find out which allele is minor allele from bed file?
plink
updated 12 days ago by
chrchang523
10k • written 13 days ago by
curious
▴ 750
0
votes
1
reply
229
views
visualize GSEA
barplot
RNA-seq
GSEA
enrichment
updated 11 days ago by
Ram
43k • written 12 days ago by
Rob
▴ 170
0
votes
2
replies
270
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 5 days ago by
GenoMax
142k • written 12 days ago by
Ximena
• 0
0
votes
1
reply
213
views
filtering before dada2
bbduk
qiime2
dada2
metagenomic
updated 12 days ago by
Ram
43k • written 12 days ago by
Valentina
• 0
0
votes
6
replies
473
views
Differential Expression Analysis using DESeq2 in R
deseq2
R
updated 12 days ago by
swbarnes2
14k • written 13 days ago by
Erina
• 0
1
vote
3
replies
321
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
10 days ago by
Lada
▴ 30
1
vote
0
replies
154
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
updated 10 days ago by
zx8754
11k • written 12 days ago by
Emilie
▴ 10
0
votes
0
replies
143
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
13 days ago by
Javier
• 0
0
votes
2
replies
295
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
updated 3 days ago by
Zhenyu Zhang
★ 1.2k • written 13 days ago by
yahn
• 0
0
votes
0
replies
135
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
13 days ago by
mikemakaveli1
• 0
2
votes
2
replies
240
views
Raw counts using stringtie
stringtie
RNA-seq
updated 13 days ago by
GenoMax
142k • written 13 days ago by
ahmad.sajad4541
• 0
0
votes
0
replies
135
views
Modify plot R mtDNA indel
plot
mtDNA
R
13 days ago by
marco.barr
▴ 120
0
votes
0
replies
332
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
13 days ago by
NorbertK
▴ 10
4
votes
2
replies
263
views
Analysis of intronic reads included scRNA-seq data
single-cell
updated 11 days ago by
Ram
43k • written 13 days ago by
carolofharvest
▴ 40
13
votes
14
replies
898
views
High Malat-1 expression in single cell data
single-cell
updated 8 days ago by
t.montserrat.ayuso
▴ 40 • written 17 days ago by
carolofharvest
▴ 40
0
votes
2
replies
279
views
Downloading older version of a tool
Alignment
tools
12 days ago by
Ruqaiya
• 0
0
votes
0
replies
155
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
13 days ago by
rustykb
▴ 20
1
vote
1
reply
202
views
DSEQ2 analysis
DESEQ2
logfoldchange
updated 11 days ago by
Ram
43k • written 13 days ago by
adi.gershon1
• 0
3
votes
5
replies
330
views
Generating mpileup file using samtools
mpileup
samtools
updated 13 days ago by
Joe
21k • written 13 days ago by
Ruqaiya
• 0
0
votes
5
replies
409
views
6 follow
What purposes can TPM values be used for?
RNA-seq
TPM
Normalization
DESeq2
updated 13 days ago by
b.contreras.moreira
▴ 180 • written 14 days ago by
JH
• 0
1
vote
3
replies
305
views
Does comparing two different groups to a common third group introduce bias in the analysis?
DESEQ
RNAseq
updated 13 days ago by
ATpoint
82k • written 13 days ago by
Qi
• 0
0
votes
0
replies
146
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
13 days ago by
Amos Bairoch
▴ 120
2
votes
3
replies
322
views
Help with choosing a model species for Augustus for a de novo assembled genome.
augustus
annotation
assembly
genome
updated 13 days ago by
dthorbur
★ 2.0k • written 13 days ago by
Vijith
▴ 30
0
votes
0
replies
160
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
13 days ago by
Jeyong
• 0
0
votes
2
replies
745
views
homer not configured properly
Homer
makeTagDirectory
updated 13 days ago by
clairechung112
• 0 • written 24 months ago by
amahdi779
• 0
1
vote
3
replies
305
views
Bedtools merge minimum overlap?
bedtools
genomics
updated 13 days ago by
Alex Reynolds
35k • written 13 days ago by
SJP
• 0
0
votes
0
replies
147
views
Empty table plot using plotGseaTable()
FGSEA
12 days ago by
Chris
▴ 280
0
votes
1
reply
206
views
VG : No reference-sense paths available in the graph; falling back to generic paths.
vg
updated 13 days ago by
anovak
▴ 120 • written 14 days ago by
Hang
• 0
1
vote
3
replies
264
views
DiffBind: no peaks in DBA
MACS2
DiffBind
ChIP-seq
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
yvonneh
▴ 10
3
votes
5
replies
377
views
Converting CRAM to FastQ
GATK
samtools
cram
SamToFastq
fastq
12 days ago by
Maverick
▴ 10
3
votes
8
replies
6.6k
views
7 follow
GATK genomicsDBimport intervals for WGS
gatk
genomicsdbimport
updated 13 days ago by
Sd
• 0 • written 5.1 years ago by
Nicolas Rosewick
11k
0
votes
2
replies
228
views
Base Quality Score Recalibration with different reference genome
SNPs
GATK
BQSR
RNA-seq
13 days ago by
dtnondorf
• 0
3
votes
8
replies
677
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 9 days ago by
Chris Dean
▴ 410 • written 13 days ago by
sovrappensiero
▴ 100
1,000 results • Page
6 of 20
Recent Votes
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
C: Splitting .vcf file
Answer: Grouping datasets in Seurat
Answer: How should I make kallisto indexes?
Comment: Why does assigning genes with biomart give me different values than using a tran
Answer: Grouping datasets in Seurat
Best tool to find potential TF binding sites within a specific DNA sequence?
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carlopecoraro2
★ 2.5k
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GenoMax
142k
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ben@f
▴ 20
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Recent Replies
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Noted! Thanks very much for your help!
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
hophuquy0944
• 0
i'm using linux. I was use 3 file.fasta to debug and it is nucleotide file, and my blast -h still work > (/data/quyho/tools/mgs2amr_tool…
Answer: Details on salmon index
by
Rob
6.5k
Hi Lorenzo, Thanks for your question. First, I'd like to clarify that several substantial updates have been made to salmon since its …
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
yura.grabovska
▴ 90
sc/snRNASeq tends to have differences in things like mitochondrial genes etc, which you can account for using tools like SCTransform but in…
Comment: Why does assigning genes with biomart give me different values than using a tran
by
bioinfo
▴ 150
Thank you! I ended up using the transcripts_to_genes instead of biomart.
Comment: How can I calculate the OS of each patient?
by
ATpoint
82k
Please be specific. Which TCGA subset, what did you try? Show code.
Answer: mitochondrial genome assembly pipeline
by
shelkmike
★ 1.2k
A good tool for mitochondrial genome assembly is GetOrganelle (https://github.com/Kinggerm/GetOrganelle)
Comment: getting exon coordinates
by
Ram
43k
Please do not use `bioinformatics` as a tag unless your post in about the field of bioinformatics itself.
Comment: Blastn error : ncbi::CObject::ThrowNullPointerException() - Attempt to access NU
by
Ram
43k
I've removed unneccessary tags - `meta` and `how-to` don't apply to this post at all, and the `forum` tag is not in use anymore.
Comment: Difference in number of reads when using duplex and simplex base calling with Do
by
GenoMax
142k
I assume you have posted this in nanopore community and/or on the dorado issues page on GitHub. Please come back and post an update once yo…
Comment: Annotating file using bcftools
by
kl
▴ 10
Do you know if there is a way to leave chr:pos in ID if there is no matching rsid based on chromosome and position, as variants have been r…
Answer: Would you bother re-mapping RNA-seq data from an old GRCh38 build to a newer ver
by
Jeremy Leipzig
22k
We get this question like clockwork every 6 weeks. I'll say it one more time: **A freeze is a freeze.** Patches are not a thing th…
Comment: Can 5' and 3' scRNAseq be processed with the same pipeline?
by
ev97
▴ 20
Thanks very much for your feedback! I will take all those things in consideration once I start the analysis! Just out of curiosity, do yo…
Answer: getting exon coordinates
by
ben@f
▴ 20
A combination of bash and awk can do the work, suppose you have the gff file annotation of your gene of interest and a text file with Gene…
Comment: getting exon coordinates
by
Pierre Lindenbaum
161k
https://www.biostars.org/p/385786/ ; <br> https://www.biostars.org/p/276608/ ; <br> https://www.biostars.org/p/411934/ ;etc... <!-- How …
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