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1,000 results • Page
3 of 20
Sort: Rank
Rank
Views
Votes
Replies
2
votes
4
replies
309
views
SnpEff annotates coding duplication as intronic?
snpeff
7 days ago by
kirill.zaslavsky
• 0
0
votes
2
replies
240
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
7 days ago by
mropri
▴ 150
0
votes
0
replies
142
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
8 days ago by
shasabhi1
• 0
0
votes
0
replies
132
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
8 days ago by
Nishat
• 0
0
votes
0
replies
157
views
what exactly is a k-mer table (remora)?
remora
basecall
8 days ago by
anne
• 0
1
vote
1
reply
173
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 8 days ago by
dsull
★ 5.8k • written 8 days ago by
niruf
• 0
0
votes
0
replies
141
views
GWAS Phenotypes
GWAS
8 days ago by
solomoncharles77
▴ 90
0
votes
2
replies
311
views
GSEA analysis in R
GSEA
R
Arabidopsis
6 days ago by
Sudip
• 0
0
votes
0
replies
122
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
8 days ago by
QX
• 0
2
votes
5
replies
430
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
7 days ago by
Bikram Kumar
• 0
0
votes
2
replies
254
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 8 days ago by
Ram
43k • written 9 days ago by
David
• 0
1
vote
2
replies
262
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
8 days ago by
bioinfo
▴ 150
0
votes
1
reply
189
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 9 days ago by
bk11
★ 2.3k • written 9 days ago by
sinhas
• 0
0
votes
1
reply
206
views
merging Seurat objects after SCT
Seurat
SCT
updated 9 days ago by
Ram
43k • written 9 days ago by
michelle.swarovski
• 0
0
votes
1
reply
201
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 9 days ago by
GenoMax
141k • written 9 days ago by
haiying.kong
▴ 360
0
votes
2
replies
263
views
RNAseq 1 control 2 different treatment
RNA-seq
8 days ago by
matteo.levorato
• 0
1
vote
0
replies
142
views
Seeking Advice on Gene Ontology Analysis for Bulk RNA-Seq Data Without Control Samples
Gene-ontology
RNA-seq
R
updated 9 days ago by
Ram
43k • written 9 days ago by
Oscar
▴ 10
0
votes
0
replies
151
views
How should I make kallisto indexes?
kallisto
updated 9 days ago by
GenoMax
141k • written 9 days ago by
bioinfo
▴ 150
2
votes
0
replies
202
views
What are good Python models/packages to predict small molecula (SMILES) binding to proteins ?
SMILES
9 days ago by
Alexander
▴ 220
1
vote
1
reply
180
views
Do I need to go back and filter my long-reads?
alignment
nanopore
filtering
QC
ONT
updated 9 days ago by
GenoMax
141k • written 9 days ago by
eesiribloom
▴ 80
0
votes
0
replies
137
views
Automated internal stop codon checker
ORF
stopcodon
internal
virus
9 days ago by
Balazs Horvath
▴ 10
0
votes
0
replies
142
views
Repeat expansion identification tools for long-read data
fragilex
repeatexpansion
long-read
fmr1
9 days ago by
adarsh_pp
▴ 40
0
votes
0
replies
151
views
FreeBayes detection capacity
reads
freebayes
long
9 days ago by
quentinperriere
• 0
0
votes
2
replies
237
views
VCF annotation with gnomADv4 using R package
annotation
gnomADv4
R
VCF
7 days ago by
DKA
▴ 40
0
votes
0
replies
161
views
Plotting heatmap of genes in each samples scRNA in Seurat
scRNA
heatmap
10 days ago by
Hien
• 0
0
votes
2
replies
284
views
Merging Outputs from plink --assoc and --hardy to Produce Table
PLINK
PANDAS
R
8 days ago by
Koketso
• 0
0
votes
0
replies
189
views
Novel cyclic peptide structure prediction
protein
structure-prediction
alphafold
peptide
updated 10 days ago by
Ram
43k • written 10 days ago by
menyawino
• 0
1
vote
3
replies
339
views
Ensembl gene id conversion
biomart
ensembl
updated 8 days ago by
ATpoint
82k • written 10 days ago by
naveedhasan2000
• 0
1
vote
2
replies
312
views
Extracting information from gff3 file produced by augustus
augustus
gff3
updated 9 days ago by
Istvan Albert
100k • written 10 days ago by
Jiang
• 0
0
votes
0
replies
187
views
Core SNP tree VS. concatenated core genome tree
phylogenetic
tree
SNP
11 days ago by
YiweiZhu
▴ 30
0
votes
2
replies
314
views
Help with understanding the identifier mapping tables in the backend of HUMAnN
metagenomics
metacyc
enzyme
biobakery
humann
11 days ago by
O.rka
▴ 710
0
votes
6
replies
544
views
PacBio adapters in transcriptome assembly from short read data?
adapter
transcriptome
sequencing
pacbio
vecscreen
9 days ago by
Dunois
★ 2.5k
4
votes
7
replies
539
views
DESeq2 Multifactor Design
RNA-seq
DESeq2
updated 11 days ago by
Ram
43k • written 12 days ago by
AHerik
▴ 20
0
votes
0
replies
185
views
Using Delly/Pindel/breakdancer for Identifying Transgene Insertion Sites in Mouse Genome
breakdancer
insertion
Pindel
variation
Delly
updated 12 days ago by
GenoMax
141k • written 12 days ago by
zec018
• 0
0
votes
0
replies
192
views
SeuratDisk: including "counts" dataset in conversion to AnnData
Seurat
SeuratDisk
AnnData
updated 12 days ago by
Ram
43k • written 12 days ago by
roussine
▴ 10
0
votes
0
replies
181
views
I am getting more annotation hits from HOMER than I have actual peaks. Is that normal?
ATAC-seq
HOMER
12 days ago by
Ronin
• 0
4
votes
13
replies
851
views
RNAseq of primary tumor and metastases in two different organ
metastases
RNA-seq
DEG
R
updated 7 days ago by
BioinfGuru
★ 1.7k • written 13 days ago by
matteo.levorato
• 0
2
votes
1
reply
243
views
VEP annotation --per_gene allele choice
VEP
updated 12 days ago by
Ram
43k • written 12 days ago by
atariw
▴ 10
0
votes
2
replies
279
views
Are GeneExpression Subtype annotations removed from TCGA-GBM?
tcga-gbm
subtyping
tcga
updated 12 days ago by
Zhenyu Zhang
★ 1.2k • written 12 days ago by
Apollonia
• 0
1
vote
1
reply
243
views
RNA seq normalization and gene gene correlation
rna-seq
pearson-correlation
vst
updated 12 days ago by
Ram
43k • written 12 days ago by
Fish
• 0
0
votes
0
replies
184
views
Snakemake fails to find conda in PBS
snakemake
12 days ago by
yixinzeng
• 0
0
votes
0
replies
188
views
KaryoPlot: Gene coverage over centromeric regions
Gene
coverage
Centromere
Bedtools
12 days ago by
Mary
• 0
0
votes
0
replies
179
views
Protein stability analysis
mutation
analysis
12 days ago by
marco.barr
▴ 80
1
vote
4
replies
386
views
what is the normal range of htseq-count output for homo sapiens RNA-Seq
Transcriptomics
htseq-count
RNA-Seq
NGS
hisat2
updated 11 days ago by
BioinfGuru
★ 1.7k • written 12 days ago by
Morteza
• 0
3
votes
1
reply
263
views
how to change the gene header names in a fasta file?
fasta
bioawk
awk
seqkit
updated 12 days ago by
Ram
43k • written 13 days ago by
rj.rezwan
• 0
0
votes
0
replies
169
views
Multiple Spike-Ins
MeRIP
Spike-In
13 days ago by
Adam
▴ 20
0
votes
0
replies
161
views
Tools for Sequence Consensus
Consensus-Sequence
bacteria
updated 13 days ago by
Ram
43k • written 13 days ago by
Reno
• 0
2
votes
2
replies
270
views
DepMap: siRNA and CRSIPR discrepancy
DepMap
updated 13 days ago by
ATpoint
82k • written 13 days ago by
Shicheng Guo
★ 9.4k
1
vote
0
replies
157
views
phasing tumor long-reads
nanopore
ONT
haplotag
phasing
tumor
13 days ago by
eesiribloom
▴ 80
0
votes
3
replies
308
views
10x GEX and ADT data analysis in Seurat
Seurat
scRNA-seq
ADT
Cite-seq
GEX
updated 11 days ago by
ATpoint
82k • written 13 days ago by
gdfsnkfns
• 0
1,000 results • Page
3 of 20
Recent Votes
Comment: clustalo - align milions of short seq, memory issue
Comment: downloading genomes in fasta format from accession ids
Comment: PCA plot (Suggestions Needed)
Answer: PCA plot (Suggestions Needed)
PCA plot (Suggestions Needed)
Comment: To get p-values for the TPM
A: Where To Download Pam50 Gene Set?
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Recent Awards •
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camillab.
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pramach1
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Adyasha
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Recent Replies
Answer: clustalo - align milions of short seq, memory issue
by
emmanouil.a
▴ 120
Hi GenoMax and Mensur Dlakic, thank you for your feedback. I'm changing approach in the way to work with a smaller number of seq.
Comment: Annovar using R package
by
Pierre Lindenbaum
161k
duplicate of your previous question: https://www.biostars.org/p/9592646/ why using R when there are shell-based tools like VEP ? slivar , …
Comment: Trouble with Pilon installation
by
Lissa Cruz Saavedra
• 0
Hi I am trying to install the software but I didn't find the way to clone from github. Could you help me with the pipeline of instruction…
Comment: Adding CB tag to bam file
by
swbarnes2
14k
I think both these programs are just adding the same tag to every line. I don't think either cares whether it's called RG or CB
Comment: PCA plot (Suggestions Needed)
by
swbarnes2
14k
Even if this was real data, the tiny numbers for the PC1 and PC2 indicate that the differences between the samples are all absolutely tiny.…
Comment: Creating Synthetic Sequences for a ML Model
by
biochugs
• 0
Thanks for the input. I'll continue to think of more ideas that may be achievable.
Comment: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
You could also try kernel PCA, which is a non-linear form of PCA, although this will be more time-consuming.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
DKA
▴ 40
I have unstranded RNA-seq data. Please share the tool with me, if you do not mind.
Comment: PCA plot (Suggestions Needed)
by
Mensur Dlakic
★ 27k
Everything that @f1f58aed said, plus that there may be no data manipulation that will give you the clusters you expected. Sometimes there a…
Answer: Creating Synthetic Sequences for a ML Model
by
Mensur Dlakic
★ 27k
It is a good idea, though I don't see how it would work in practice. I think you will encounter at least one additional problem on top of …
Answer: PCA plot (Suggestions Needed)
by
Jeremy
▴ 890
Right now, the WT samples are clustering together, but you have one mutant sample off by itself, which could be an outlier. How did you sc…
Comment: Adding CB tag to bam file
by
GenoMax
141k
@yokofakun had written this: https://www.biostars.org/p/336965/ https://github.com/ruqianl/appendCB may also be useful.
Comment: Troubleshooting RNA-seq data with DNA contamination
by
GenoMax
141k
Please post information about your tool as a `tools` category post. Don't wait/ask other users to ask you.
Comment: Adding CB tag to bam file
by
Maria
• 0
Sorry for the delay in my answer, I got sidetracked. I am using ```samtools addreplacerg -r "@RG\tID:$cell" -o $cell.bam -h $LINE``` bu…
Answer: Troubleshooting RNA-seq data with DNA contamination
by
haibol2017
▴ 10
We just developed a R package to tackle this problem. Do you have stranded or unstranded RNA-seq data contaminated with gDNA? If you wou…
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