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347 results • Page
3 of 7
Sort: replies
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0
votes
2
replies
145
views
novel and know mir156 and mir172
a
updated 14 hours ago by
gayachit
▴ 200 • written 18 hours ago by
Fadmo
• 0
0
votes
2
replies
358
views
How can I have the structure of a gene (or haplotypes of a gene) on the top of the LD plot on Haploview
LDplot
Haploview
HaplotypeBlocks
LinkageFormat
20 days ago by
mona.patoughi
• 0
0
votes
2
replies
311
views
Alphafold2 Colab
AlphaFold
updated 24 days ago by
dthorbur
★ 1.7k • written 26 days ago by
Preeti
• 0
0
votes
2
replies
231
views
How to get genes in a gene set in msigdb?
msigdb
16 days ago by
Chris
▴ 260
0
votes
2
replies
199
views
how to run limma for large datasets
R
HPC
biostatistics
statistics
updated 2 days ago by
Ram
43k • written 3 days ago by
Bioinfonext
▴ 460
1
vote
2
replies
440
views
RNA-seq differential expression across multiple tissues, 2 trials, and 2 conditions
RNA-seq
DESeq
EdgeR
Batch-effect
DEGs
10 days ago by
BioinfGuru
★ 1.6k
2
votes
2
replies
205
views
A pipeline for prediction and annotation of obelisks
rna-seq
updated 22 hours ago by
Pierre Lindenbaum
160k • written 1 day ago by
fred.s.kremer
▴ 110
1
vote
2
replies
1.2k
views
Multi-fasta file for gffread
gffread
gtf
fasta
updated 6 days ago by
alnam
▴ 10 • written 2.4 years ago by
Vitor1
▴ 120
0
votes
2
replies
287
views
PopGenome lost individual information
PopGenome
1 day ago by
Yixuan
• 0
0
votes
2
replies
238
views
How to interpret merged_calls result of command line from CNVpytor
CNVpytor
updated 18 days ago by
GenoMax
140k • written 18 days ago by
Nannapat
• 0
0
votes
2
replies
233
views
nf-core/rnaseq, problem with ensembl reference
nfcore
nextflow
ensembl
rnaseq
9 days ago by
Filip
• 0
1
vote
2
replies
253
views
WGCNA for co-expression network analysis
WGCNA
20 days ago by
Priya
• 0
1
vote
2
replies
284
views
How to extract mutations in a particular gene from the VCF file of whole genome
NGS
mutations
VCF
21 days ago by
saamar.rajput
▴ 70
1
vote
2
replies
544
views
Applicability of the SoupX ambient mRNA decontamination technique to fixed and/or multiplexed scRNAseq experiments
SoupX
scRNA-seq
8 days ago by
e.r.zakiev
▴ 170
2
votes
2
replies
332
views
Would you recommend me any tool to assign protein family membership to an aminoacidic fasta file?
protein-annotation
fasta
updated 8 days ago by
Dunois
★ 2.5k • written 7 weeks ago by
v.berriosfarias
▴ 140
1
vote
2
replies
222
views
Deseq generating warning "the model matrix is not full rank"
deseq
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
MAPK2
▴ 40
0
votes
2
replies
304
views
BMI as a continuous variable is my outcome, which type data i should put to calculate
transcriptomics
29 days ago by
jiefei
• 0
1
vote
2
replies
229
views
BWA MEM Alignment mapped small part of the reads!!
bwa
mem
updated 1 day ago by
bioruffo
▴ 40 • written 2 days ago by
Bunit
• 0
2
votes
2
replies
262
views
compare dimplot(single cell)
DEG
scRNAseq
12 days ago by
kayah
• 0
2
votes
2
replies
224
views
singlecell annotation
scRNA-seq
annotation
1 day ago by
kayah
• 0
1
vote
2
replies
238
views
Upset plot
upsetplot
10 days ago by
Chris
▴ 260
0
votes
2
replies
229
views
Problem merging plink files for somatic variants.
plink
somatic
vcf
18 days ago by
Palgrave
▴ 110
2
votes
2
replies
211
views
ggplot2 installation
ggplot2
updated 16 days ago by
rpolicastro
13k • written 16 days ago by
safeassli
• 0
0
votes
1
reply
146
views
Snakemake wrapper issue
fastqc
snakemake
updated 16 days ago by
Ram
43k • written 16 days ago by
Matvii Mykhailichenko
• 0
0
votes
1
reply
200
views
Getting error in alignment using STAR
STAR
Error
updated 5 days ago by
Michael
54k • written 5 days ago by
pavithra.bioinformatics
• 0
0
votes
1
reply
139
views
How to perform GO enrichment analysis for assembled sequence ?
GO-enrichment
Gene-Ontology
updated 2 days ago by
Ram
43k • written 3 days ago by
Sony
▴ 10
0
votes
1
reply
127
views
Can I have multiple active GDC download tokens?
TCGA
updated 2 days ago by
GenoMax
140k • written 2 days ago by
mrk
• 0
0
votes
1
reply
370
views
Strange distribution of logFC values after searching for significantly differentially expressed genes
limma
23 days ago by
Robert
• 0
2
votes
1
reply
143
views
Computing the neighborhood graph in single cell pipeline
single-cell
knn
updated 17 days ago by
ATpoint
81k • written 17 days ago by
QX
• 0
0
votes
1
reply
236
views
updateR() error
R
update
updated 10 days ago by
dthorbur
★ 1.7k • written 13 days ago by
marco.barr
▴ 30
0
votes
1
reply
172
views
BRIG coverage.graph issues
BRIG
sam
updated 10 days ago by
Pierre Lindenbaum
160k • written 10 days ago by
dlera.lozano
• 0
0
votes
1
reply
152
views
Understanding Uncommon Genotype Formats in VCF Files Generated by nf-core RNAvar Pipeline
genotype
rnaseq
updated 16 days ago by
Pierre Lindenbaum
160k • written 16 days ago by
ASid
▴ 40
0
votes
1
reply
191
views
Running Pangolin
Pangolin
Splicing
updated 19 days ago by
Ram
43k • written 20 days ago by
Sruthi
• 0
0
votes
1
reply
141
views
dbsnp flanks information
dbsnp
updated 1 day ago by
Pierre Lindenbaum
160k • written 1 day ago by
sskimvd
• 0
1
vote
1
reply
207
views
lncRNA and ncPEPs identification
lncRNA
updated 13 days ago by
Yahel
• 0 • written 15 days ago by
atharvakarkare14
▴ 10
0
votes
1
reply
221
views
deepTools computeMatrix output import into R for enrichment calculations
R
deeptools
computeMatrix
deepTools
updated 12 days ago by
Pierre Lindenbaum
160k • written 12 days ago by
eeb74
• 0
0
votes
1
reply
185
views
Computing mid parent value for DE analysis
EdgeR
limma
DESeq2
updated 19 days ago by
Gordon Smyth
★ 6.9k • written 8 weeks ago by
pl23
• 0
0
votes
1
reply
210
views
Merging snpEff file and extracting novel mutations
sars-cov-2
phylogenetic
novelmutations
updated 29 days ago by
Pierre Lindenbaum
160k • written 4 weeks ago by
realtreeecat
• 0
0
votes
1
reply
125
views
Bed file
bedfile
updated 14 days ago by
Pierre Lindenbaum
160k • written 14 days ago by
Jeet
• 0
0
votes
1
reply
175
views
Resources regarding Proteomics (In-Silico)
proteomics
docking
protein
molecular-simulation
updated 8 days ago by
Ram
43k • written 9 days ago by
Saurabh
• 0
0
votes
1
reply
61
views
Merging featureCounts output for different species
featureCount
RNAseq
updated 4 hours ago by
andrebolerbarros
• 0 • written 4 hours ago by
Christian
• 0
2
votes
1
reply
207
views
Disease Prevalence Database/Disease Incidence Database
prevalence
updated 6 days ago by
Ram
43k • written 7 days ago by
Shicheng Guo
★ 9.4k
0
votes
1
reply
199
views
Pathway activity in Bulk-RNA-SEQ analysis
R
RNA-seq
transcriptomics
updated 13 days ago by
jared.andrews07
★ 16k • written 13 days ago by
PBC
▴ 10
0
votes
1
reply
224
views
Resolution of ambiguous calls in germline vcf
vcfs
germline
qc
updated 26 days ago by
Jeremy Leipzig
22k • written 27 days ago by
Raygozak
★ 1.4k
0
votes
1
reply
124
views
DMRcate for sequencing data
DMRcate
DNA-methylation
differential-methylation
updated 7 days ago by
Basti
★ 1.9k • written 17 days ago by
alejandrarodrigu21
• 0
1
vote
1
reply
243
views
BAM to CRAM and BAM recover with smaller size
BAM
samtools
CRAM
updated 12 days ago by
GenoMax
140k • written 12 days ago by
geocarvalho
▴ 360
0
votes
1
reply
159
views
Mutation, MAF, CPTAC-3
CPTAC
mutation
updated 22 days ago by
marco.barr
▴ 30 • written 22 days ago by
Rob
▴ 170
0
votes
1
reply
36
views
Flow Cytometry Data Analysis by Seurat
Seurat
updated 1 hour ago by
ATpoint
81k • written 2 hours ago by
gdfsnkfns
• 0
0
votes
1
reply
145
views
Autodock tools error - The requested operation requires lifting
Autodock
MGLTools
updated 2 days ago by
zx8754
11k • written 2 days ago by
DOMENICA ALEXANDRA
• 0
0
votes
1
reply
10
views
(sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
RNA-seq
dataset
updated just now by
GenoMax
140k • written 16 minutes ago by
chiditatawmbi
• 0
347 results • Page
3 of 7
Recent Votes
Comment: Interproscan taking so much time
Answer: Interproscan taking so much time
Comment: Volcano Plot Output Inquiry: Graphs Facing Down
A: Crispr-cas9 screen analysis mageck
A: Crispr-cas9 screen analysis mageck
Crispr-cas9 screen analysis mageck
Answer: Issue with making local BLAST database
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Commentator
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Devon Ryan
104k
Popular Question
to
amitpande74
▴ 20
Scholar
to
Pierre Lindenbaum
160k
Popular Question
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beacamara
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blur
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ATpoint
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Recent Replies
Comment: FindAllMarkers not working (Error (data layers are not joined. Please run JoinL
by
Nitin
• 0
I tried that too. It did not work.
Comment: (sc)RNA-seq dataset for these cell lines: HEK293, HeLa, PC3 and U2OS
by
GenoMax
140k
Try SRA-explorer with search terms you want. Guide here: https://www.biostars.org/p/366721/ Check these portals: https://singlecell.broad…
Comment: Issue with making local BLAST database
by
Begonia_pavonina
▴ 140
Thank you @genomax, if I have well understood the `retmax` parameter and 10000 entries limitation are linked to the R package, and not to t…
Comment: Nanopore data filtering using fastp
by
emilydolivo97
• 0
thank you , this is my code : import sys import os import subprocess class FastpFiltering: def __init__(self, input_folder, fastp_ou…
Comment: Nanopore data filtering using fastp
by
GenoMax
140k
You can also use `reformat.sh` from [**BBMap suite**][1]. Look at sampling options. [1]: https://sourceforge.net/projects/bbmap/
Comment: calculate mismatch rate from VCF file
by
Pierre Lindenbaum
160k
> I was using it but the output file was too big pipe the output
Comment: Nanopore data filtering using fastp
by
dthorbur
★ 1.7k
Share code and an example please.
Comment: calculate mismatch rate from VCF file
by
Dora
▴ 10
I was using it but the output file was too big, so that I thought the vcf file was more efficient. But now I know that I can stop working o…
Comment: Interproscan taking so much time
by
Mohamed Abderrahmane
▴ 10
Thank you for your reply. I have just executed the computation with parallelization as you mentioned, and I will observe the differences. H…
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Of course ... But as 'expected' the range `range=chr8:127794533-128101253` in the output sequence file belongs to: LF385466, LF385467, MA62…
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
Can you select the output format as sequence instead of BED?
Comment: struggle to get fasta files from ucsc goldenPath
by
Lila M
★ 1.2k
Could you please elaborate how to retrieve the sequences directly from the table browser? Thanks!
Comment: struggle to get fasta files from ucsc goldenPath
by
GenoMax
140k
If coordinates in your BED file refer to chromosomal locations then you need to use the whole genome file and get those sections by the met…
Comment: How to Use Biostars, Part-I: Questions, Answers, Comments and Replies
by
Istvan Albert
100k
maybe it would work better to ask the OP to post their question as a new one and delete this answer after, if you delete the post they ca…
Answer: Issue with making local BLAST database
by
GenoMax
140k
By default only 20 entries are returned if you don't set the `retmax` parameter. You will not want to do this via R since you will be limit…
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