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122,001 results • Page
617 of 2441
Sort: Rank
Rank
Views
Votes
Replies
8
votes
14
replies
3.8k
views
6 follow
kallisto pseudoalignment rate is lower than literature
pseudoalignment
kallisto
RNA-seq
4.2 years ago by
johnsonqinz
• 0
4
votes
1
reply
3.3k
views
logFC or logCPM?
edgeR
updated 4.2 years ago by
seidel
11k • written 4.2 years ago by
mariaargote995
▴ 10
0
votes
0
replies
569
views
calculating heterozygozity from phased genome
phased
heterozygozity
genome
calculation
4.2 years ago by
roger.huerlimann
▴ 10
1
vote
0
replies
1.8k
views
SingleR annotations
cell
seurat
singler
single
10x
updated 4.2 years ago by
GenoMax
154k • written 4.2 years ago by
jyotikataria2008
▴ 10
2
votes
4
replies
1.4k
views
Replacing a character in multiple fasta files within a folder
replace
find
and
4.2 years ago by
alexis.diaz
• 0
2
votes
1
reply
1.0k
views
Ramachandran Plot
region
disallowing
Ramachandran
updated 4.2 years ago by
Hyper_Odin
▴ 320 • written 4.2 years ago by
1961012
▴ 20
0
votes
1
reply
1.5k
views
ClinicalTrial data in CSV format
xml
database
csv
ClinicalTrials.gov
updated 4.2 years ago by
Jeremy Leipzig
23k • written 4.2 years ago by
ahmetolcum
• 0
9
votes
7
replies
4.3k
views
Averaging duplicates of a gene in RNA-Seq dataset
expression
differential
average
R
rna-seq
updated 4.2 years ago by
biomon
▴ 60 • written 4.3 years ago by
mohammedtoufiq91
▴ 270
0
votes
1
reply
1.7k
views
ChiP Seq differential analysis with Homer
Differential
Fold-change
Homer
Deseq2
updated 4.2 years ago by
biomon
▴ 60 • written 4.3 years ago by
B612
• 0
0
votes
2
replies
1.3k
views
Matching the file names with exposure file in TCGA
FPKM
exposure
TCGA
updated 2.6 years ago by
Ram
45k • written 4.3 years ago by
nazaninhoseinkhan
▴ 530
2
votes
2
replies
1.3k
views
hypergeometric test for gene feature enrichment on population frequency data
enrichment
hypergeometric
R
phyper
fisher
updated 4.2 years ago by
LauferVA
4.8k • written 4.3 years ago by
code_evo
▴ 30
6
votes
10
replies
2.7k
views
Perl script on rna G quadruplex
perl
G-quadruplex
rna
updated 14 months ago by
Ram
45k • written 4.3 years ago by
isha.lily20
▴ 10
5
votes
5
replies
2.2k
views
Sum up value within a interval
genome
4.2 years ago by
CWL
• 0
0
votes
6
replies
2.1k
views
annotate sites with gene info
annotation
updated 4.2 years ago by
Alex Reynolds
36k • written 4.3 years ago by
Rdeveloop
• 0
0
votes
2
replies
1.3k
views
GSEA for multiple groups
gsea
4.2 years ago by
An Ignorant Wanderer
• 0
12
votes
5
replies
7.3k
views
How to generate start & end coordinates for each chromosome of human ref genome in bed. format (0-based index)
bed
bedtools
bioconductor
genome
updated 4.2 years ago by
Jorge Amigo
14k • written 5.6 years ago by
Alewa
▴ 190
2
votes
4
replies
2.0k
views
hifiasm assembled contigs alignment to a reference genome sequence
hifiasm
4.2 years ago by
sulemanqasimbtech
• 0
4
votes
4
replies
2.8k
views
How to extract Locus tag from GeneIDs in NCBI for soybean database.
RNASeq
Soybean
tag
Locus
ID
Glyma
4.3 years ago by
b.g.tamang
▴ 20
0
votes
4
replies
1.5k
views
Running alignment using Bowtie by setting specific maximum number of mismatches
mismatch
alignment
bowtie
4.2 years ago by
jahanshahi.amin
• 0
14
votes
10
replies
2.8k
views
How to get the name of a protein by knowing only the RefSeq accession number?
BLAST
RefSeq
NCBI
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
Alex
▴ 10
9
votes
4
replies
5.4k
views
TCR RNAseq Single Cell Data Analysis
TCR
ImmunoSeq
RNA-Seq
Single Cell
Paired
updated 8.3 years ago by
carina.dehner
• 0 • written 8.9 years ago by
bioinformatics.cancer
▴ 260
0
votes
1
reply
1.4k
views
How to extract amino acids from receptor-ligand complex pdb?
docking
dlg
vina
pdb
autodock
updated 4.3 years ago by
Jiyao Wang
▴ 380 • written 4.4 years ago by
mmarcell
• 0
0
votes
4
replies
2.2k
views
Finding Binding Site Residues
protein
residue
binding
site
updated 4.3 years ago by
Jiyao Wang
▴ 380 • written 4.3 years ago by
antoniaa
▴ 30
3
votes
1
reply
1.1k
views
usearch11 cluster_fast option
usearch
proteins
clustering
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
g.papp-co
▴ 30
0
votes
0
replies
1.2k
views
struct2geno error
analysis
population
R
4.3 years ago by
genya35
▴ 50
2
votes
5
replies
3.0k
views
How to pass custom software specific variables to nf-core/sarek nextflow pipeline?
wgs
updated 4.1 years ago by
Phil Ewels
★ 1.5k • written 4.3 years ago by
optimistsso4co3
▴ 140
0
votes
3
replies
1.2k
views
How long time does it take the Alignment of 3 groups hg using RNA-Seq Alignment App in illumina?
analysis
RNA
Seq
4.3 years ago by
Bioinformatics1
▴ 10
2
votes
1
reply
1.2k
views
DAVID database for gene ontology
DAVID
geneontology
4.3 years ago by
Vaani
• 0
11
votes
5
replies
1.9k
views
Publishing RNA sequencing data analysis scripts on Github before or after Publication?
github
4.2 years ago by
m.sadman.sakib
▴ 120
1
vote
0
replies
1.1k
views
Job:
PhD Candidate, Using Ontologies to build a Knowledge Graph for Molecular Interactions of Nanoparticles (Maastricht/NL)
owl
phd
knowledge
ontology
netherlands
graph
4.3 years ago by
Egon Willighagen
5.4k
0
votes
0
replies
1.3k
views
Job:
Postdoctoral Researcher in Bioinformatics/Cheminformatics, using OpenAPI, FAIR, and Docker for predictive toxicology and risk assessment (Maastricht/…
openapi
toxicology
netherlands
postdoc
docker
4.3 years ago by
Egon Willighagen
5.4k
3
votes
18
replies
5.0k
views
Help creating Deseq2 count matrix from separate files
or
Sample
matrix
updated 4.2 years ago by
Ram
45k • written 4.3 years ago by
Nai
▴ 50
0
votes
0
replies
458
views
the mutual information matrix computed from minet R package>1
minet
4.3 years ago by
wei
• 0
0
votes
0
replies
1.1k
views
GSEA time series analysis - cls file format?
GSEA
cls
4.3 years ago by
garfield320
▴ 20
5
votes
2
replies
3.1k
views
BCL2Fastq when I5 index is UMI
UMI
bcl2fastq
demultiplex
4.2 years ago by
ccagg
▴ 60
1
vote
2
replies
6.2k
views
Spike-in normalization with Cut&Tag data
deeptools
normalization
ChIP-Seq
cutandtag
updated 4.3 years ago by
ATpoint
89k • written 5.2 years ago by
hina.bandukwala
• 0
1
vote
2
replies
1.9k
views
Haplotype phasing with Beagle on microarray output VCF, tunning suggestions?
beagle
phasing
microarray
4.3 years ago by
jpablo
• 0
2
votes
0
replies
765
views
Stringtie on non model organism - how to best proceed for DE analysis?
Salmon
Stringtie
DESeq
transcriptome
rna-seq
4.3 years ago by
Shred
★ 1.6k
0
votes
0
replies
510
views
Use All Clusters Expression in One Set with User Defined Phenotypes in rank_gene_groups
Scanpy
Python
updated 4.2 years ago by
Ram
45k • written 4.3 years ago by
pb
• 0
0
votes
2
replies
1.3k
views
Annotating draft genome of a Trichomonad species
Trichomonads
Genome
annotation
MAKER
FINDER...
updated 4.3 years ago by
Michael
56k • written 5.7 years ago by
shinasplitzo
• 0
4
votes
13
replies
41k
views
6 follow
[main_samview] fail to read the header from sample.bam
alignment
updated 3.3 years ago by
Qboy
▴ 10 • written 7.6 years ago by
sambioinfo2018
▴ 20
1
vote
0
replies
638
views
Comparing distribution of microarray data to that of RNA-seq data
distribution
4.3 years ago by
english.server
▴ 300
1
vote
4
replies
1.5k
views
3d structure without PDB
python
biopython
updated 2.6 years ago by
Ram
45k • written 4.3 years ago by
dachi
• 0
3
votes
3
replies
1.1k
views
P value signficancy
GEO
GEO2R
updated 2.7 years ago by
Ram
45k • written 4.3 years ago by
fahim
▴ 20
1
vote
1
reply
2.0k
views
Comparison of ratio of expression between two genes across samples
RNA-Seq
TPM
normalization
relative abundance
updated 3.9 years ago by
Martin Modrák
▴ 80 • written 4.9 years ago by
guillepalou4
▴ 20
1
vote
4
replies
1.6k
views
Isoseq3 : Floating point exception
PacBio
isoseq
updated 4.3 years ago by
GenoMax
154k • written 4.3 years ago by
slin023
▴ 20
0
votes
0
replies
827
views
How to add optional parameters to the Rest API VEP query
API
ensemble
VEP
REST
4.3 years ago by
davidjohngreen
• 0
3
votes
7
replies
2.0k
views
Get per-nucleotide mapping position for each mapped reads from bam file
mapping
nucleotide
position
4.3 years ago by
Changhao Li
• 0
2
votes
2
replies
1.5k
views
An issue in creating a bubble plot using ggplot2
blubbleplot
ggplot2
issue
updated 3.0 years ago by
Nitin Narwade
★ 1.7k • written 4.3 years ago by
f.finamore
• 0
0
votes
0
replies
852
views
Co-binning with Metabat2, how do I map my reads with BWA?
Metabat2
Co-binning
BWA
4.3 years ago by
howla1ke
• 0
122,001 results • Page
617 of 2441
Recent Votes
Difficulty running FoldX in linux
Answer: Difficulty running FoldX in linux
Answer: Differences between published differential gene expression results and own analy
Answer: Differences between published differential gene expression results and own analy
Comment: Problems with PacBio's Improved Phased Assembler (IPA)
Comment: Differences between published differential gene expression results and own analy
A: Fold change - a final explanation
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yarrowmadrona
▴ 10
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45k
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SomeOne
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★ 30k
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Comment: headers missing in efetch results for SRA database
by
Leela
• 0
Please note that this is still a problem in the recent version in `conda` (v24.0)
Comment: Difficulty running FoldX in linux
by
strayeroliver
• 0
Thank you very much for your help.
Comment: Problems with PacBio's Improved Phased Assembler (IPA)
by
Billy Rowell
▴ 520
Completely understand. I hope this helps then!
Comment: Checkm results differ from database info
by
Mensur Dlakic
★ 30k
Impossible to answer with the little information you provided. It's like saying that your soufflé didn't rise, and we are supposed to guess…
Comment: Active site using castpfold
by
Mensur Dlakic
★ 30k
Please don't take my comment the wrong way. Docking ligands is a serious endeavor that includes many preparatory steps, a use of highly so…
Comment: Problems with PacBio's Improved Phased Assembler (IPA)
by
Panos
★ 1.8k
Thanks! I will try further downgrading snakemake (and python).. Actually, I have already tried `hifiasm` which worked perfectly (as always…
Comment: downloading raw bam files from pacbio sequencer
by
GenoMax
154k
https://www.biostars.org/u/151541/ look through some of the top entries from this search for subread BAM's. Here is one example: https://do…
Comment: Difficulty running FoldX in linux
by
Mensur Dlakic
★ 30k
I think `1ubq_Repair_1.pdb` is an intermediate file, and the other 3 files matter. But I use FoldX rarely, so you will have to verify this …
Comment: Difficulty running FoldX in linux
by
strayeroliver
• 0
That's great, @mensur. Thank you. I have a run that operates on 1ubq_Repair.pdb and produces a 'Dif_1ubq_Repair.fxout' now, even with numbe…
Comment: Problems with PacBio's Improved Phased Assembler (IPA)
by
Billy Rowell
▴ 520
Is there a reason you'd like to use IPA over, for instance, hifiasm? I'd recommend starting with hifiasm. For pbipa, try downgrading to s…
Answer: Active site using castpfold
by
dthorbur
★ 3.1k
This is very similar to your recent [post](https://www.biostars.org/p/9615406/) - if you aren't going to provide the protein example for a …
Answer: Differences between published differential gene expression results and own analy
by
Zhenyu Zhang
★ 1.3k
1. When you said "the same dataset", are you sure about the files are the same, or you just mean the same list of patients? There are many …
Answer: downloading raw bam files from pacbio sequencer
by
Arup Ghosh
3.4k
Try: https://www.google.com/search?q=site:https://downloads.pacbcloud.com/public/dataset/+%22subreads%22
Comment: downloading raw bam files from pacbio sequencer
by
GenoMax
154k
If they are not available at PacBio site then your chances of getting them are going to be significantly reduced. Only other source may be …
Comment: downloading raw bam files from pacbio sequencer
by
pranavdatar01
• 0
Yes, I did check. They don't have any.
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