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116,475 results • Page
2 of 2330
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Votes
Replies
0
votes
0
replies
248
views
Looking for an explanation as to what the Peak Score is from HOMER, not finding any answers on Biostars yet
Homer
ATAC-seq
1 day ago by
Ronin
• 0
4
votes
2
replies
1.7k
views
How to convert SAM/BAM file to GTF/GFF file?
GTF
SAM
BAM
GFF
minimap2
updated 1 day ago by
Dr.Animo
▴ 130 • written 11 months ago by
BioinfoBee
• 0
2
votes
7
replies
657
views
Removing duplicates
duplicates
ONT
minimap2
updated 5 hours ago by
joe
▴ 500 • written 1 day ago by
quentinperriere
• 0
0
votes
1
reply
161
views
Annotating a dataset with gnomAD v4 using Hail
Python
Sequencing
Hail
Exome
Annotation
updated 1 day ago by
DKA
▴ 40 • written 1 day ago by
james.melhorn
• 0
3
votes
4
replies
334
views
biomaRt error for different R version
biomaRt
R
updated 16 hours ago by
GenoMax
141k • written 1 day ago by
manaswwm
▴ 490
0
votes
1
reply
149
views
Freyja plot error
Freyja
updated 1 day ago by
Ram
43k • written 1 day ago by
Adyasha
• 0
1
vote
2
replies
160
views
Interpretation of combined P values - RNA microarray meta analysis
metaanalysis
R
microarray
DExMA
combinedP
1 day ago by
hagl
▴ 10
0
votes
0
replies
119
views
BIOM format can contain tabular data ?
BIOM
phyloseq
biomformat
R
1 day ago by
chemokine-1
▴ 10
0
votes
4
replies
410
views
How to reduce the variation of CIBERSORTx results?
CIBERSORTx
deconcolution
21 hours ago by
feather-W
• 0
0
votes
1
reply
178
views
Job:
Consultant to update a Snakemake workflow with the new Kubernetes executor plugin for Snakemake 8
Kubernetes
DevOps
executor
AWS
Snakemake
updated 1 day ago by
Michael
54k • written 1 day ago by
jonrkarr
▴ 100
0
votes
2
replies
179
views
Bedmethyl file format
bedmethyl
methylation
updated 1 day ago by
GenoMax
141k • written 1 day ago by
njornet
▴ 20
0
votes
0
replies
127
views
sequence table for DADA2 chimera filtering
OTU
sequencetable
DADA2
1 day ago by
Ali
• 0
2
votes
4
replies
266
views
SnpEff annotates coding duplication as intronic?
snpeff
1 day ago by
kirill.zaslavsky
• 0
0
votes
2
replies
204
views
Calculating percentage of cells proliferating in single cell rna seq data
statistics
scRNA-seq
proliferation
1 day ago by
mropri
▴ 150
5
votes
4
replies
2.8k
views
genefu for PAM50 prediction
RNA-Seq
breast cancer
subtyping
updated 2 days ago by
hamarillo
▴ 70 • written 5.6 years ago by
silviajserrano
▴ 50
3
votes
10
replies
574
views
Piping samtools to R
R
NGS
bash
samtools
2 days ago by
joe
▴ 500
2
votes
2
replies
204
views
How to filter columns in a raw sparse matrix in R
matrix
R
updated 2 days ago by
bk11
★ 2.3k • written 2 days ago by
bgbs
• 0
3
votes
7
replies
375
views
Integration of transcriptomics and proteomics: difficult matching names
rna-seq
tmt
nomenclature
proteomics
2 days ago by
ntsopoul
▴ 60
0
votes
0
replies
121
views
Input into WGCNA and Error on constructNetworks on RNA-Seq data - unique rownames
rownames
RNA-Seq
WGCNA
unique
2 days ago by
shasabhi1
• 0
0
votes
0
replies
118
views
How to summarize dbCAN3 results
dbCAN
CAZy
CAZyme
dbCAN3
dbCAN2
2 days ago by
Nishat
• 0
3
votes
3
replies
375
views
trouble using sequenceTubeMap in chromium installed on WSL
vg
2 days ago by
ayushm64
• 0
0
votes
0
replies
128
views
what exactly is a k-mer table (remora)?
remora
basecall
2 days ago by
anne
• 0
3
votes
6
replies
10k
views
List of species in RepeatMasker Tool (species parameter)
RepeatMasker
Masking
updated 2 days ago by
Bioinfotec
▴ 10 • written 7.5 years ago by
nut_B
▴ 10
1
vote
6
replies
336
views
Rename multiple fastq.gz files
fastq
next-gen
updated 2 days ago by
shenwei356
8.4k • written 2 days ago by
Jérémie
• 0
1
vote
1
reply
154
views
Help/Direction Needed for Data Analysis of RNA
Sequencing
RNA-seq
DNA-Seq
updated 2 days ago by
dsull
★ 5.8k • written 2 days ago by
niruf
• 0
0
votes
0
replies
150
views
Job:
Ensembl Outreach Project Leader
ebi
embl
genomics
ensembl
2 days ago by
Ben_Ensembl
★ 2.4k
2
votes
3
replies
236
views
Bwa sampe - BGI
Bwa-sampe
BGI
updated 2 days ago by
GenoMax
141k • written 2 days ago by
lorena9132
• 0
0
votes
0
replies
148
views
News:
Final Call - Bioinformatics Pipeline Development with Nextflow (May 27-29, 2024)
workshop
RNA-seq
nextflow
DNA-seq
updated 2 days ago by
Ram
43k • written 2 days ago by
David Langenberger
11k
0
votes
0
replies
123
views
GWAS Phenotypes
GWAS
2 days ago by
solomoncharles77
▴ 90
4
votes
2
replies
231
views
Forum:
Bioinformatics: Where do I start
Sequencing
updated 2 days ago by
Ram
43k • written 2 days ago by
Adi
▴ 10
0
votes
2
replies
271
views
GSEA analysis in R
GSEA
R
Arabidopsis
19 hours ago by
Sudip
• 0
1
vote
2
replies
232
views
Visualization of PROKKA Annotation Result?
PROKKA
Annotation
updated 2 days ago by
Joe
21k • written 3 days ago by
ferdinand
▴ 10
0
votes
2
replies
338
views
Which experiments generate Position Frequency Matrix?
Position-Frequency-Matrix
1 day ago by
arriyaz.nstu
▴ 30
2
votes
2
replies
347
views
I am new to single cell analysis. Can RNA velocity (spliced/unspliced) be calculated solely from the raw file (count matrix) provided in the Suppleme…
GEO
velocity
count-matrix
updated 2 days ago by
Ram
43k • written 2 days ago by
Spring
• 0
0
votes
0
replies
105
views
Add geno header to VariantAnnotation objects
nichenet
scRNA-seq
2 days ago by
QX
• 0
5
votes
4
replies
248
views
I'm new to cell ranger. Can single cells prepared with a protocol other than the 10x genomics protocol not be processed with cell ranger?
cellranger
scRNA-seq
10x
2 days ago by
Spring
• 0
2
votes
5
replies
338
views
Where to find the homopolymer regions bed file for Hg002 genome?
simple-repeats
hg002
bed
homopolymer-regions
1 day ago by
Bikram Kumar
• 0
1
vote
1
reply
273
views
WGCNA network from Adjacency or TOM matrix
WGCNA
network
updated 2 days ago by
andres.firrincieli
3.6k • written 6 days ago by
Milly
• 0
0
votes
1
reply
196
views
Error in edgeR/Deseq2 Analysis
r
edger
updated 2 days ago by
ATpoint
81k • written 2 days ago by
Ravita
• 0
0
votes
2
replies
200
views
Getting marker genes for cell types
clustering
marker-genes
umap
2 days ago by
orzrzlyo
▴ 20
0
votes
1
reply
196
views
gene body coverage with RSeqQC
rna-seq
qc
updated 2 days ago by
BioinfGuru
★ 1.7k • written 3 days ago by
wiscoyogi
▴ 40
0
votes
2
replies
225
views
Statistical Advice Needed for RNAseq Data Analysis
Statistical-Significance
Genomics
RNA-seq
Data-Analysis
updated 2 days ago by
Ram
43k • written 3 days ago by
David
• 0
0
votes
1
reply
173
views
Using adonis to include a random effect
mixed-model
adonis
updated 3 days ago by
LChart
3.9k • written 3 days ago by
leranwangcs
▴ 120
1
vote
3
replies
397
views
how to get the variance explained by the independent variable from multivariate distance matrix regression model with random effect?
multivariate-distance-matrix
regression
updated 3 days ago by
LChart
3.9k • written 4 days ago by
leranwangcs
▴ 120
1
vote
2
replies
232
views
Can I compare kallisto counts from samples with different amount of reads?
RNA-seq
kallisto
2 days ago by
bioinfo
▴ 150
0
votes
1
reply
170
views
How to get the reference panel sites for TOPMed hg37 and 38
Imputation
updated 3 days ago by
bk11
★ 2.3k • written 3 days ago by
sinhas
• 0
1
vote
5
replies
320
views
Best way to deal with overlapping read names in merged BAM files
picard
MarkDuplicates
3 days ago by
shpak.max
▴ 50
0
votes
1
reply
186
views
merging Seurat objects after SCT
Seurat
SCT
updated 3 days ago by
Ram
43k • written 3 days ago by
michelle.swarovski
• 0
0
votes
1
reply
165
views
Two databases: Human Microbiome Project and MGnify
Microbiome
databases
updated 3 days ago by
GenoMax
141k • written 3 days ago by
haiying.kong
▴ 360
0
votes
2
replies
237
views
RNAseq 1 control 2 different treatment
RNA-seq
2 days ago by
matteo.levorato
• 0
116,475 results • Page
2 of 2330
Recent Votes
Bedtools merge but only if intersection exists
Answer: Korean reference file
Comment: Korean human genome reference file
C: samtools sort bam file
A: samtools sort bam file
Answer: Downloaded pdb's on rcsb.org
Comment: Downloaded pdb's on rcsb.org
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Recent Replies
Comment: miRNAs quantification using mirdeep2 tool
by
Ashok
• 0
thank you for your reply https://github.com/rajewsky-lab/mirdeep2/blob/master/TUTORIAL.md i saw this github tutorial for miRNA quantifica…
Comment: Load a full GFF3 into annotation track using arrow (Apollo)
by
cmdcolin
★ 3.8k
Hi there, I let a developer know of this thread and they said they can check it out next week. Feel free to post to the https://github.com/…
Comment: How to get the reference panel for UKBB
by
航太郎
• 0
Thanks for your guide!
Comment: Removing duplicates
by
joe
▴ 500
I'd try those OP @samuel recommends My guess is you're new to ONT, fast5 is the 'raw data' which is current over time...other than generat…
Comment: RNA seq differential expression analysis
by
swbarnes2
14k
No. Find a tutorial, try it, then if you have specific questions, ask of the galaxy help site.
Answer: Adding CB tag to bam file
by
swbarnes2
14k
Shouldn't you use PicardTools for this?
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
Sure. Or, one could do: bash try.bash "Homo sapiens" AHR | xargs -I v_pdb curl -s -o v_pdb.pdb https://files.rcsb.org/view/v_pdb.pdb
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you so much
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
This may be the best option. Get the PDB ID's $ ./get.sh "Mus musculus" AHR 4M4X 5NJ8 5V0L 8H77 Then use `curl` to g…
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
It gives you the first 25 results though. I'll see if I can change that. EDIT: I've updated that number to 250. I'm hoping you won't need …
Comment: Downloaded pdb's on rcsb.org
by
iamsmor
• 0
thank you very much
Answer: Downloaded pdb's on rcsb.org
by
Ram
43k
I'm going to build off of OP's query and give them a simple script: ```bash organism=$(echo $1 | sed 's/ /%20/g') gene=$2 curl -s https:/…
Comment: miRNAs quantification using mirdeep2 tool
by
GenoMax
141k
This question does not make complete sense. If you have your own data files why do you need deep sequencing reads? Genome (can be download…
Comment: Downloaded pdb's on rcsb.org
by
GenoMax
141k
For a non-programmer using the search builder link included above may be the best option. Even that is not very user friendly.
Comment: Downloaded pdb's on rcsb.org
by
Ram
43k
That's how they seem to have written their query - automating that is a bit of a pain though as it takes a crazy JSON as input.
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