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224 results • Page
4 of 5
Sort: replies
Rank
Views
Votes
Replies
0
votes
1
reply
193
views
Java class error message when using BBDuk
rna-seq
bbduk
updated 2 days ago by
GenoMax
136k • written 2 days ago by
milewski
• 0
0
votes
1
reply
184
views
Is GeSeq currently unavailable?
GeSeq
updated 2 days ago by
GenoMax
136k • written 2 days ago by
zy
• 0
0
votes
1
reply
198
views
WGCNA Dendrogram Branch missing from modules
WGCNA
dendrogram
hdWGCNA
updated 2 days ago by
andres.firrincieli
3.5k • written 2 days ago by
mhale
• 0
0
votes
1
reply
156
views
Java error while running HiCDC overview code
R
Juicer
HiC
HiCDCPlus
updated 6 days ago by
Brian Bushnell
20k • written 6 days ago by
isMM
• 0
0
votes
1
reply
152
views
Annotation GTF/GFF Arabidopsis thaliana
Arabidopsis
GFF
GTF
Annotation
6 days ago by
enriquesan
• 0
0
votes
1
reply
237
views
Tutorials for Spatial Transcriptomics
ST-Seq
Scanpy
Seurat
updated 1 day ago by
CTLong
▴ 50 • written 2 days ago by
saqlain
▴ 90
1
vote
1
reply
152
views
What's the acceptable threshold in Quality Assessment for Genome Assemblies?
control
genome
QUAST
quality
assembly
kbase
updated 1 day ago by
liorglic
★ 1.3k • written 1 day ago by
JaneZheng0406
• 0
0
votes
1
reply
203
views
Cibersort input data
cibersort
updated 23 hours ago by
Kaia
• 0 • written 2 days ago by
Maryam
• 0
1
vote
1
reply
293
views
Forum:
want to work in open source project/project in bioinformatics
project
updated 6 days ago by
Ram
41k • written 16 days ago by
Afeef
• 0
0
votes
1
reply
215
views
Are 10x cellranger-arc ATAC bam files deduplicated?
10x
single-cell
updated 6 days ago by
Ram
41k • written 9 days ago by
WaterMetal
• 0
0
votes
1
reply
149
views
News:
Course: Genome Assembly and Annotation
Biodiversity
Genome-Assembly
Genome-Annotation
Long-reads
updated 6 days ago by
Ram
41k • written 11 days ago by
carlopecoraro2
★ 2.4k
0
votes
1
reply
352
views
News:
RNA-Seq Data Analysis Workshop (March 11 - 14, 2024 in Berlin, Germany)
NGS
RNA-Seq
Workshop
4 days ago by
David Langenberger
10k
0
votes
1
reply
161
views
absolute running error: Error in if (!is.na(res)) { : the condition has length > 1
ABSOLUTE
error
4 days ago by
qiuting
• 0
0
votes
1
reply
184
views
Cell ranger multi for demultiplexing FB files and GEX files
cellranger
updated 4 days ago by
Ram
41k • written 5 days ago by
Shloka
• 0
0
votes
1
reply
197
views
CHIPSEQ Analysis , DiffBind Parameters
DiffBind
ChIP-seq
updated 4 days ago by
Rory Stark
★ 2.0k • written 11 days ago by
DINESHR
• 0
1
vote
1
reply
229
views
How to use Nextflow to call scripts from different environments?
anaconda
conda
nextflow
updated 4 days ago by
Ram
41k • written 5 days ago by
O.rka
▴ 710
1
vote
1
reply
1.3k
views
How to interpret the discrepancy of assignment rate in featurecounts using forward and reverse strand protocols
RNAseq
updated 5 days ago by
charles.feigin
• 0 • written 7 weeks ago by
xinrantian
▴ 20
0
votes
0
replies
118
views
RNA secondary structure for GRCH38 transcriptome
dot-bracket-notation
human
RNA-secondary-structure
GRCH38
6 days ago by
Saad Khan
▴ 420
0
votes
0
replies
144
views
Infer ancestry for RNA-seq data
plink
admixture
ancestry
updated 2 days ago by
Ram
41k • written 2 days ago by
Matthew Chang
• 0
0
votes
0
replies
142
views
how to run the compare_genomes for comparative analysis
genome
orthofinder
evolution
2 days ago by
rj.rezwan
• 0
0
votes
0
replies
110
views
Need to PrepSCTfindMarker again after subset if the original object has already been normalized?
FindMarker
Seurat
6 days ago by
Adrian
• 0
0
votes
0
replies
501
views
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Species
StringTie
Orthogroups
Transcript
Assembly
2 days ago by
dtnondorf
• 0
0
votes
0
replies
116
views
ASEReadCounter output wrong number of coverage
ASEReadCounter
5 days ago by
junhuili
• 0
0
votes
0
replies
137
views
News:
Course - Introduction to R Shiny
R
Data-Visualisation
Shiny
updated 6 days ago by
Ram
41k • written 19 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
106
views
GAPIT p-value significance threshold
GAPIT
p-value
GWAS
6 days ago by
Clayton
• 0
0
votes
0
replies
151
views
Extract upstream and downstream 50bp nontemplated sequences from a position
search
sequences
nontemplated
motif
6 hours ago by
Ty
• 0
0
votes
0
replies
145
views
News:
Course - RNAseq in non-model organisms
Pacbio
RNA-seq
Nanopore
updated 6 days ago by
Ram
41k • written 21 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
126
views
News:
University of Connecticut Single Cell RNA-seq Workshop December 12-15, 2023
expression
singlecell
rnaseq
4 days ago by
mia.nahom
▴ 10
0
votes
0
replies
107
views
cosinoRmixedeffect: an R package for mixed-effects cosinor models
interactionmodel
cosinor
mixedeffect
circadian
4 days ago by
Agnia
• 0
0
votes
0
replies
107
views
Tool:
retroSeeker: discovering novel retrotransposons in humans and any species
element
Expression
Evolution
Retrotransposon
Mobile
4 days ago by
lsp03yjh
▴ 850
0
votes
0
replies
112
views
Test for multiplicative effect in mendelian randomization?
R
mendelian_randomization
GWAS
2 days ago by
clairvoyant
• 0
0
votes
0
replies
205
views
Haplotype network/phylogeny of 1000 genomes project
haplotype
1000Genomes
phylogeny
updated 3 days ago by
Ram
41k • written 5 months ago by
Morgan
• 0
0
votes
0
replies
701
views
Generating variant read count matrix, total read count matrix and binary/ternary mutaion matrix for SNV from scDNAseq FASTQ files
SNV
mutationMatrix
tumorPhylogeny
scDNAseq
mutaion
4 days ago by
supernovamik
• 0
0
votes
0
replies
95
views
how to run GSEA with spesific background
RNA-seq
GSEA
updated 3 days ago by
Ram
41k • written 4 days ago by
Chava
• 0
0
votes
0
replies
105
views
megablast taxonomy assign in blobtools
blobtools
5 days ago by
bs
• 0
0
votes
0
replies
195
views
News:
GWAS course
R
GWAS
updated 6 days ago by
Ram
41k • written 17 days ago by
carlopecoraro2
★ 2.4k
1
vote
0
replies
128
views
Tutorial:
CITEseq tutorial
CITEseq
Alevin
Seurat
5 days ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
104
views
News:
New version of ElasticBLAST (1.2.0) available from NCBI
ElasticBLAST
NCBI
BLAST
3 days ago by
PeterC_NCBI
▴ 370
0
votes
0
replies
110
views
use GEOparse to download series supplemental files?
gse
geoparse
python
geoquery
geo
3 days ago by
mk
▴ 290
0
votes
0
replies
120
views
Expression differs when running plotTranscripts vs boxplot of FPKM or coverage values (R)?
R
updated 6 days ago by
Ram
41k • written 6 days ago by
boone5jones
• 0
0
votes
0
replies
123
views
Confusing results from FindConservedMarkers in Seurat
10XGenomics
3 days ago by
pm2012
▴ 140
0
votes
0
replies
106
views
Differing output: vcftools' --weir-fst-pop and R hierfstats package's varcomp.glob()
vcftools
hierfstats
fst
6 days ago by
S
• 0
0
votes
0
replies
93
views
Using Metagenome Samples for HNSCC analysis
Linux
DESEQ2
SRA
Bioinformatics
ComputationalBiology
1 day ago by
Ozymandeus
▴ 30
0
votes
0
replies
169
views
News:
Course - Introduction to Bayesian Data Analysis
R
Statistics
Bayesian
Regression-Modeling
updated 6 days ago by
Ram
41k • written 5 weeks ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
32
views
Need Help Mapping Probe IDs to Gene Symbols
microarray
2 hours ago by
maryam.kh
• 0
0
votes
0
replies
97
views
Tutorial:
download metadata using GEOquery
biology
GEO
metadata
computational
1 day ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
171
views
News:
Course: Genome Assembly using Oxford Nanopore Sequencing
Genome-Assembly
Nanopore
updated 6 days ago by
Ram
41k • written 28 days ago by
carlopecoraro2
★ 2.4k
0
votes
0
replies
100
views
inverse normal p-value combination results giving NaN.
inverse
meta-Analysis
p-value
rnaseq
normal
4 days ago by
sehriban.buyukkilic
• 0
0
votes
0
replies
100
views
Job:
Postdocs in Anaerobic Microbial Consortia – DTU Chemical Engineering
Microbiology
microbiology
Biochemistry
Anaerobic
4 days ago by
info
▴ 80
0
votes
0
replies
150
views
Converting txt.gz to PLINK bim
S-LDSC
file
LDSC
format
3 days ago by
X
• 0
224 results • Page
4 of 5
Recent Votes
Are Variable Features ranked in seurat?
Answer: protein clustering and pangenome tools
Answer: get gene name from rsID
Answer: get gene name from rsID
Comment: MinKNOW software installation doubt for MinION Nanopore sequencing
Comment: Minimum requirements for a laptop to do rna seq analysis
Best-suited unit of expression to perform between-sample comparison
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Recent Replies
Answer: Autocompleting paths within scripts
by
Michael
53k
Not really a Bioinformatics question but generally very useful: [vim can do that][1] [type some prefix of path] <Ctrl-x><Ctrl-f> ![e…
Answer: How can I obtain the DNA sequences of each CDS for several genbank files?
by
Raphaëlle
• 0
Hello, Thank you very much for your quick reply. That was indeed the issue! Another question: is there a simple way of automating this …
Answer: Cluster sub-set analysis using Seurat
by
j.gleixner
▴ 10
There now is also `Seurat::FindSubCluster`
Comment: How can i control the cluster number in scRNASeq clustering by Seurat package
by
j.gleixner
▴ 10
There is now also Seurat::BuildClusterTree that makes this easier.
Answer: How can i control the cluster number in scRNASeq clustering by Seurat package
by
j.gleixner
▴ 10
If you want to get a certain number of clusters without resorting to trying different settings for the resolution parameter, you can firs…
Answer: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I will also try this `fasttree`
Comment: i ues schicexplorer's hicbuildmatrix code complains that two sam files do not ha
by
1125195245
• 0
I tried using bowtie2's --reorder command to output a sam file for each of the two files, and then used both sam files to build the matrix,…
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I used MEGA CC (comand line option) but there is no option to specify threads in its `--help` manual . And default thread is 4
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
The average length of fasta sequences is ~300aa length. I can't exclude any sequences as I have to provide them nomenclature aslo on the ba…
Comment: How to speed-up to contruct phylogenetic tree
by
Nelo
▴ 20
I used Raxml for a trial fasta file of about only 33 sequences as: `raxmlHPC-PTHREADS-AVX -f a -T 80 -m PROTGAMMAWAG -n test1 -s bittergou…
Comment: i ues schicexplorer's hicbuildmatrix code complains that two sam files do not ha
by
ATpoint
78k
It's bad practice to add the question to the title and only a screenshot as question. The error is clear. Did you try what it suggests, and…
Answer: What apps can read large FASTQ files on Windows?
by
i.sudbery
18k
There are a number of bioinformatics workbenches that will run under windows, and will allow you to analyse fastq files. Some examples …
Comment: Multi-factor designs in DiffBind
by
g.persic1991
• 0
Dear Rory, thanks a lot for your help. It's work, indeed now I'm able to find (as expected) more DB. The only things "strange" is that I…
Comment: How to cluster .faa files?
by
dthorbur
▴ 890
I agree with Joe, it's hard to tell what you want. But here are some general suggestions: 1. [OrthoFinder](https://github.com/davidemms/Ort…
Comment: Is interleaved Fastq files the same as interlaced fastq
by
Joe
21k
No need to post a comment, you can just edit your original post after the fact
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