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122,034 results • Page
1 of 2441
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0
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0
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51
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Python deconvolution tools for bulk RNA-seq data
RNA-seq
bulk-rna-seq
Deconvolution
python
transcriptomics
8 hours ago by
AlexStar
▴ 200
1
vote
1
reply
93
views
Unique insertion sites Calculation from Himar1 C9 based TnSeq
Kossivi
updated 10 hours ago by
GenoMax
154k • written 14 hours ago by
Kossivi
• 0
2
votes
5
replies
171
views
BWA-MEM with an array of files
alignment
array
BWA-MEM
updated 12 hours ago by
LChart
5.1k • written 14 hours ago by
garcesj
▴ 50
847
votes
170
replies
215k
views
112 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
handbook
training
updated 15 days ago by
Biostar
3.6k • written 8.9 years ago by
Istvan Albert
103k
1
vote
4
replies
148
views
reference-guided assembly tools for short read data?
genomics
assembly
bioinformatics
13 hours ago by
Hani
• 0
0
votes
0
replies
63
views
interpretation of the results obtained with digital PCR
dPCR
16 hours ago by
Lorenzo
• 0
1
vote
3
replies
140
views
MOuse Testis Enhancer region
enhancer
1 hour ago by
Bioinformatics_16
• 0
0
votes
0
replies
94
views
Job:
Sr. Manager, Clinical Data Science at InterVenn Biosciences
statistics
glycoproteomics
proteomics
machine-learning
omics
10 hours ago by
Daniel
• 0
2
votes
1
reply
162
views
Modeling/simulations using SNPs data
SNP
updated 1 day ago by
Dave Carlson
★ 2.2k • written 1 day ago by
Gonzalo
• 0
2
votes
1
reply
158
views
Strugling on the 3'rule of HGVS
notation
hgvs
variants
updated 1 day ago by
Jeremy Leipzig
23k • written 1 day ago by
lacb
▴ 120
13
votes
17
replies
4.8k
views
Extract fastq sequences based on date/time (which is in the header)
sequence
fastq
updated 1 day ago by
zhanxw
▴ 20 • written 7.1 years ago by
a.b.g
▴ 10
2
votes
5
replies
3.0k
views
Filter nanopore fastq files by start time
nanopore
fastq
filter
start time
updated 1 day ago by
zhanxw
▴ 20 • written 6.3 years ago by
sendhelp
▴ 10
1
vote
3
replies
316
views
Choosing enrichment analysis tool
DAVID
Metascape
Enrichr
updated 1 day ago by
i.sudbery
22k • written 3 days ago by
Marlene
• 0
3
votes
4
replies
198
views
Discrepancy in Q-score assessment of ONT reads in Nanopore and third-party software repors
seqkit
q-score
fastqc
16s-wf
nanoplot
1 day ago by
k-tarasov
▴ 10
4
votes
4
replies
564
views
How to create a consensus of a contig with samtools or bbmap?
contig
bbmap
consensus
samtools
genome
updated 1 day ago by
jkbonfield
★ 1.3k • written 12 days ago by
marongiu.luigi
▴ 770
1
vote
1
reply
182
views
Validating snRNA-seq cell type by correlating with other datasets
RNA-seq
scRNA-seq
snRNA-seq
updated 1 day ago by
ATpoint
89k • written 2 days ago by
Ben
• 0
0
votes
1
reply
130
views
Configuration file for DSP WTA
DSP
updated 1 day ago by
GenoMax
154k • written 1 day ago by
Petesview
▴ 10
0
votes
0
replies
94
views
News:
1st Berlin Winter School in RNA-Seq Data Analysis (Dec 8-11, 2025)
Transcriptomics
RNA-Seq
Expression
Differential
1 day ago by
ecSeq Bioinformatics
▴ 20
0
votes
2
replies
219
views
What is the length of the longest ORF appearing in reading frame 2 of any of the sequences?
python
2 days ago by
fra.r.silvestro
▴ 10
0
votes
0
replies
130
views
Does the weights file stay the same for a different model organism
machine
learning
weights
bioinformatics
updated 2 days ago by
GenoMax
154k • written 2 days ago by
Sharma
• 0
0
votes
2
replies
183
views
HDOCK Server Error!
HDOCK
Docking
1 hour ago by
Jannatul Ferdous
• 0
3
votes
1
reply
177
views
Variant Normalization
vcf
updated 2 days ago by
Istvan Albert
103k • written 2 days ago by
spesks
• 0
1
vote
2
replies
547
views
Should differential expression analysis be incorporated in cross validation for training machine learning models?
RNA-seq
DEA
TCGA
Learning
Machine
2 days ago by
yordany.perdigon
• 0
0
votes
0
replies
139
views
News:
Autumn School in Bioinformatics – Online, 20–24 October
NGS
Phylogenomics
RNAseq
Singularity
Docker
updated 2 days ago by
Pierre Lindenbaum
166k • written 2 days ago by
Physalia-courses
★ 2.7k
0
votes
1
reply
183
views
Issue with Snippy 4.6.0
Snippy
Core.vcf
SNP
updated 2 days ago by
GenoMax
154k • written 2 days ago by
bioinfo_enthusiast
• 0
0
votes
2
replies
231
views
Cells from normal sample were incorrectly classified as tumor cells using copykat
copykat
scRNA-seq
cell
tumor
21 hours ago by
tujuchuanli
▴ 130
0
votes
1
reply
185
views
NOVOPlasty assembly fails with “INVALID SEED” using first read as seed
mitochondria
Assembly
Genome
Novoplasty
updated 2 days ago by
GenoMax
154k • written 2 days ago by
Buddha
• 0
3
votes
1
reply
255
views
1 vs 1 DEG analysis in scrna seq data
DEG
updated 3 days ago by
ATpoint
89k • written 3 days ago by
carolofharvest
▴ 50
20
votes
13
replies
1.3k
views
6 follow
GUI commercial software for 10x single cell gene expression analysis
single-cell
software
commercial
gui
3 days ago by
firestar
★ 1.7k
1
vote
0
replies
204
views
Tool:
ORFanage: by-reference protein annotation and comparison for transcriptome assembly
orf
rna-seq
assembly
annotation
transcriptome
4 days ago by
Ales
▴ 90
0
votes
10
replies
678
views
Tool:
Brave: Bioinformatics Reactive Analysis and Visualization Engine
Docker
R
Nextflow
Python
React
1 day ago by
Edward
• 0
0
votes
2
replies
491
views
scVI vs Harmony, which is better for cell type based clustering in brain tissue?
harmony
scVI
single
cell
updated 4 days ago by
ATpoint
89k • written 9 days ago by
biotrekker
▴ 110
1
vote
0
replies
231
views
News:
Manual Genome Curation using PretextView course
Genome-Assembly
PretextView
HI-C
Manuel-Curation
5 days ago by
Physalia-courses
★ 2.7k
4
votes
11
replies
872
views
DESeq2 on metagenome KO counts
abundance
KEGG
KO
deseq
metagenome
gene
updated 5 days ago by
Aleksandra
▴ 190 • written 6 days ago by
young_bioinformatician
▴ 240
0
votes
0
replies
272
views
News:
Introduction to Processing and Analysis of Spatial Multiplexed Proteomics Data
Spatial
Proteomics
omics
updated 6 days ago by
GenoMax
154k • written 6 days ago by
oliverhooker
▴ 110
2
votes
1
reply
320
views
FACS quality control based on size and doublet detection in scRNA-seq
single-cell
rna-detection
FACS
doublet
scRNA-seq
updated 3 days ago by
Ram
45k • written 6 days ago by
carolofharvest
▴ 50
1
vote
1
reply
385
views
combine VCF from diploid reference/haplotypes for the same sample
bcftools
combine
VCF
updated 5 days ago by
cmdcolin
★ 4.3k • written 6 days ago by
Matteo Ungaro
▴ 130
4
votes
4
replies
446
views
How to handle TrEMBL proteins without gene annotation in plasma proteomics?
biomarker
uniprot
proteomics
annotation
trembl
updated 6 days ago by
Elisabeth Gasteiger
★ 2.4k • written 7 days ago by
Luwell
• 0
7
votes
2
replies
374
views
Recommendations for 200 SNP markers genotyping
sequencing
DNA
genotyping
marker
updated 6 days ago by
Aleksandra
▴ 190 • written 6 days ago by
PolenP
▴ 10
0
votes
3
replies
472
views
Interpreting genomic features distribution for CUT&RUN peaks
cut_and_run
genomic
features
updated 5 days ago by
rfran010
★ 1.7k • written 8 days ago by
Rozita
▴ 40
0
votes
3
replies
433
views
hisat2 error-Paired end reads not equal or lack of RAM/disk space?
end
fastq
paired
updated 3 days ago by
lieven.sterck
16k • written 6 days ago by
aj123
▴ 130
1
vote
2
replies
371
views
Reasonable number of SNPs in a bacterial genome.
SNP
bacteria
updated 3 days ago by
michael.ante
★ 4.0k • written 7 days ago by
yesquokkan
• 0
2
votes
6
replies
756
views
Difficulty running FoldX in linux
DDG
foldx
updated 7 days ago by
strayeroliver
• 0 • written 9 days ago by
strayeroliver
▴ 10
0
votes
2
replies
397
views
Active site using castpfold
activesite
castpfold
Docking
updated 7 days ago by
Mensur Dlakic
★ 30k • written 7 days ago by
Ria
• 0
5
votes
12
replies
1.3k
views
6 follow
Differences between published differential gene expression results and own analysis on RNA-seq data
R
TCGA
LIMMA
updated 7 days ago by
Zhenyu Zhang
★ 1.3k • written 14 days ago by
vernonlim98
• 0
1
vote
4
replies
531
views
Problems with PacBio's Improved Phased Assembler (IPA)
pacbio
hifi
assembly
genome
6 days ago by
Panos
★ 1.8k
0
votes
6
replies
587
views
downloading raw bam files from pacbio sequencer
raw
bam_file
raw_subreads
reads
updated 7 days ago by
GenoMax
154k • written 8 days ago by
pranavdatar01
• 0
0
votes
0
replies
274
views
Best way to map biological pathways to cancer hallmarks using PLMs (without building models)?
PLM
mapping
LLM
extraction
Relation
7 days ago by
DEPANSHI
• 0
1
vote
2
replies
613
views
installation of package ‘DESeq2’ had non-zero exit status
Bioinformatics
updated 7 days ago by
GenoMax
154k • written 7 days ago by
Sarita
• 0
0
votes
1
reply
326
views
Checkm results differ from database info
Checkm
updated 3 days ago by
Ram
45k • written 7 days ago by
alevbozan18
• 0
122,034 results • Page
1 of 2441
Recent Votes
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
Answer: Choosing enrichment analysis tool
Answer: reference-guided assembly tools for short read data?
Answer: BWA-MEM with an array of files
Comment: BWA-MEM with an array of files
Answer: MOuse Testis Enhancer region
Dependent samples in DESeq2 - How to incorporate random factor?
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Recent Replies
Comment: MOuse Testis Enhancer region
by
Bioinformatics_16
• 0
@genomax Do you have access to this list? If so, could you please share it? I need it urgently.
Comment: HDOCK Server Error!
by
Jannatul Ferdous
• 0
Tried that but unfortunately, the problem still persists :( Thanks for your response though!
Answer: Unique insertion sites Calculation from Himar1 C9 based TnSeq
by
LChart
5.1k
While Himar1 inserts in TA motifs, the library is generated following restriction enzyme treatment (Mmrl) and ligation. The Mmrl sequence i…
Comment: Is it possible to do standard GSEA in R?
by
mbramble
• 0
See discussion at https://support.bioconductor.org/p/9142651/#9142680 concerning issues with preranked gsea.
Comment: BWA-MEM with an array of files
by
LChart
5.1k
For solution 1, because bwa streams the data, you can save some space by using a named pipe: ```bash mkfifo Sample_23/concat.R1.fq.gz find…
Comment: reference-guided assembly tools for short read data?
by
Hani
• 0
Either de novo or reference based genome assembly using Illumina PE short reads
Comment: reference-guided assembly tools for short read data?
by
lieven.sterck
16k
which purpose specifically?
Comment: reference-guided assembly tools for short read data?
by
Hani
• 0
In regards to your comment about synteny analysis, I suspected that would be the case. In regards to tools for these purposes, do you perso…
Comment: BWA-MEM with an array of files
by
lieven.sterck
16k
aha, but bwa mem only takes at best 1 pair of fastq files as input, not a whole list. So to achieve this efficiently do what https://www.b…
Answer: reference-guided assembly tools for short read data?
by
lieven.sterck
16k
Not silly at all and done before many times. So yes that is a valid approach. There are certainly a number of tools around that can do this…
Comment: BWA-MEM with an array of files
by
garcesj
▴ 50
None in particular (that's why I didn't indicate it). It just gives back the BWA-MEM help.
Answer: BWA-MEM with an array of files
by
Pierre Lindenbaum
166k
solution 1: merge each R1 and R2 files into one. Beware, the order of the fastq files must be the same find Sample_23 -type f -name …
Comment: BWA-MEM with an array of files
by
lieven.sterck
16k
what is the (error) message you get, if any?
Comment: MOuse Testis Enhancer region
by
Bioinformatics_16
• 0
![enter image description here][1] [1]: /media/images/0241beed-c410-47b0-b8e2-43534232
Answer: MOuse Testis Enhancer region
by
GenoMax
154k
It is not just you the site appears to be down right now: https://downforeveryoneorjustme.com/enhanceratlas.org?proto=http&www=1
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