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12,301 results • Page
2 of 247
Sort: Rank
Rank
Views
Votes
Replies
1
vote
10
replies
611
views
Add stats to the plot
R
1 day ago by
Ghada
• 0
0
votes
4
replies
224
views
Fewer sites in vcf than in reference genome despite Emit_All_Sites argument
GATK
UnifiedGenotyper
1 day ago by
shpak.max
▴ 50
2
votes
4
replies
250
views
Allele count of 2 for homoplasmic MT variants in VCF
Variant-Calling
GATK
VCF
17 hours ago by
Arton
▴ 10
1
vote
3
replies
189
views
downloading chemical database from ChEMBL
ChEMBL
PyRMD
Virtual-Screening
updated 1 day ago by
GenoMax
142k • written 1 day ago by
s
• 0
0
votes
3
replies
179
views
Where are the illumina adapters on Trimmomatic take from?
rna-seq
trimmomatic
updated 1 day ago by
GenoMax
142k • written 1 day ago by
bioinfo
▴ 150
1
vote
2
replies
169
views
Multiplexing for pooled CRISPR screen sequencing
multiplex
CRISPR-screen
Illumina
19 hours ago by
Tuấn Anh
• 0
2
votes
4
replies
1.1k
views
Is it possible to run CibersortX with a very small number of samples?
cibersortx
2 hours ago by
Aspire
▴ 330
1
vote
3
replies
291
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
1 day ago by
Pegasus
▴ 100
0
votes
2
replies
193
views
Comparing Analysis Strategies for scRNA-seq Data: Separate vs. Merged Analysis of Spleen Samples from Different Conditions
Seurat
scRNA-Seq
Single-Cell
1 day ago by
Shukai
• 0
1
vote
3
replies
194
views
Question about samtools view flags (paired reads vs. properly paired reads)
samtools
updated 1 day ago by
Pierre Lindenbaum
162k • written 1 day ago by
mrk
• 0
0
votes
3
replies
236
views
z-score of gene set
z-score
scRNA
gene-set
1 day ago by
Hien
• 0
3
votes
2
replies
201
views
converting transcript IDs (Ensembl) to gene symbols in R
RNA-seq
updated 1 day ago by
GenoMax
142k • written 2 days ago by
ashkan
▴ 160
0
votes
0
replies
104
views
Linking AMR Genes to Taxonomy in Soil Metagenomics
metagenomics
bacteria
wgs
AMR
resistome
updated 1 day ago by
GenoMax
142k • written 1 day ago by
LuciaNhu
• 0
1
vote
2
replies
181
views
How can we convert a vcf to fasta, so that I can blast some genes against that whole genome sequences?
blast
fasta
vcf
gene
updated 1 day ago by
Ram
44k • written 1 day ago by
Harshita
• 0
3
votes
0
replies
117
views
Comparing ATAC-seq narrowPeak Files from Chicken and Mouse
liftOver
ATAC-seq
csaw
updated 1 day ago by
Ram
44k • written 1 day ago by
Rafael Soler
★ 1.2k
0
votes
0
replies
126
views
Job:
PhD position for metagenomics analysis at the University of Udine
metagenomics
updated 1 day ago by
Ram
44k • written 1 day ago by
Fabio Marroni
★ 3.0k
3
votes
5
replies
472
views
Practical Haplotype Graph v2 not finding correct paths
Pangenome
PHG
graph
2 days ago by
beantkapoor16
▴ 10
0
votes
1
reply
132
views
DRAGEN gVCF files and joint calling GATK-GenomicsDB
DRAGEN
GenomicsDB
updated 2 days ago by
DBScan
▴ 310 • written 2 days ago by
brunomiwa
• 0
0
votes
0
replies
90
views
Last step of metagenome analysis before visualization
metagenome
python
analyis
2 days ago by
Ayda Ecem
• 0
0
votes
3
replies
161
views
Generating a Bed file from a Fasta file
bed
NullSeq
updated 1 day ago by
Ram
44k • written 2 days ago by
pirku
• 0
0
votes
3
replies
1.8k
views
Running STRUCTURE from command line
STRUCTURE
updated 1 day ago by
Ram
44k • written 3.0 years ago by
giulia.trauzzi
▴ 10
1
vote
3
replies
557
views
Pruning Phylogenetic Trees and Bootstrap Values
phylogenetics
bootstrap
updated 2 days ago by
Klaus S
▴ 160 • written 5 weeks ago by
Zeng Hao
▴ 40
0
votes
0
replies
88
views
Calculated LAI is too large
annotation
LAI
assembly
TE
genome
2 days ago by
Yao
▴ 30
1
vote
1
reply
735
views
Herald:
The Biostar Herald for Monday, November 01, 2021
herald
written 2.6 years ago by
Biostar
2.8k
19
votes
10
replies
7.3k
views
7 follow
T2T-CHM13 "complete" human genome gff/gtf annotation file
genomics
written 3.0 years ago by
noodle
▴ 590
0
votes
0
replies
88
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
2 days ago by
dawnyipingzou
• 0
0
votes
4
replies
229
views
Where to find old version of GATK best practice
gatk
1 day ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
115
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 2 days ago by
Pierre Lindenbaum
162k • written 2 days ago by
Peter Chung
▴ 200
0
votes
0
replies
93
views
News:
Online course- Advanced Python for Life Sciences
Python-Programming
Data-Visualisation
Machine-Learning
updated 1 day ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
0
votes
1
reply
126
views
CreateSeuratObject taking very long
seurat
updated 2 days ago by
Nitin Narwade
★ 1.6k • written 2 days ago by
eae6d2e7
• 0
1
vote
2
replies
209
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
2 days ago by
ojaswinipandey
• 0
1
vote
4
replies
298
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 2 days ago by
Ram
44k • written 2 days ago by
Harshita
• 0
2
votes
4
replies
239
views
Filter Genome for Specific Sites
bedtools
updated 2 days ago by
Ram
44k • written 2 days ago by
Anita
• 0
0
votes
3
replies
252
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 2 days ago by
marco.barr
▴ 130 • written 3 days ago by
Mohamed Samir
▴ 30
1
vote
1
reply
128
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 2 days ago by
GenoMax
142k • written 2 days ago by
niruf
• 0
0
votes
0
replies
96
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 2 days ago by
Ram
44k • written 2 days ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
135
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
2 days ago by
Biostar
2.8k
3
votes
5
replies
439
views
Super ehancers
enhancers
updated 1 day ago by
jared.andrews07
★ 17k • written 21 days ago by
Oburah
• 0
0
votes
2
replies
182
views
vcf phasing
beagle
WhatsHap
phasing
1 day ago by
safeassli
▴ 10
0
votes
2
replies
209
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
2 days ago by
sainavyav22
• 0
0
votes
1
reply
608
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 3 days ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
193
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 2 days ago by
Ram
44k • written 3 days ago by
Sony
▴ 10
0
votes
3
replies
204
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 2 days ago by
Ram
44k • written 3 days ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
98
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 2 days ago by
Ram
44k • written 3 days ago by
ev97
▴ 20
0
votes
1
reply
141
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 3 days ago by
marco.barr
▴ 130 • written 3 days ago by
sooni
▴ 20
0
votes
1
reply
106
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 3 days ago by
GenoMax
142k • written 3 days ago by
jinyi
• 0
0
votes
0
replies
83
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
3 days ago by
V_Vibes
• 0
0
votes
0
replies
176
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 2 days ago by
Ram
44k • written 3 days ago by
JorgeVallejo
▴ 20
0
votes
0
replies
104
views
transcriptome annotation
annotation
trinity
transcriptome
updated 2 days ago by
Ram
44k • written 3 days ago by
Asim Bin Arshad
• 0
0
votes
5
replies
231
views
Why most genes have high padj values
RNA-seq
DEG
updated 2 days ago by
Ram
44k • written 3 days ago by
mnx0723
• 0
12,301 results • Page
2 of 247
Recent Votes
Comment: log2 fold change in RNA-seq analysis
Comment: log2 fold change in RNA-seq analysis
Answer: Ideal PC configurations and operating system for bioinformatics laboratory
correct way of analyzing cell proportions in singlecell data
Comment: How to interpret this plotMDS of three disease clusters?
gseGO: no term enriched under specific pvalueCutoff
Answer: Error with BiocParallel. No barcodes files found
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Recent Replies
Answer: Z score
by
Akash D
▴ 50
I made this. Z scored on log2FC? will anyone support me on this? 3 groups A,B,C
Comment: log2 fold change in RNA-seq analysis
by
i.sudbery
19k
There is no such thing as a fold change of -2. Fold change is expression_in_condition_A/expresssion_in_condition_B as expression is a…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
DE with 100s of samples (particulalry if your experiemental design is more complex than 2 condition DE) can stretch consumer grade hardware…
Comment: Error with BiocParallel. No barcodes files found
by
NTerway
• 0
Thank you for your help! I will try this out. I am trying to implement a collaborator's pipeline on my data and they only use SCE, scran an…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
ATpoint
82k
Once you have the counts any n is possible on a regular analysis-grade laptop or workstation. Even hundreds of samples. It's really the pre…
Comment: Error with BiocParallel. No barcodes files found
by
ATpoint
82k
You just tell the function to remove the prefix for you. Not on the actual file. Then you can add this information to the SCE, like `sce$da…
Comment: log2 fold change in RNA-seq analysis
by
May Ling
• 0
Thank you for your response. I apologize if my understanding is incomplete. I would like to ask: if I have a fold change of -2, how can I c…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
i.sudbery
19k
Yeah, a standard 3x3 bulk experiement is very analysable on pretty much most good consumer laptops these days.
Comment: Error with BiocParallel. No barcodes files found
by
NTerway
• 0
Thanks for the explanation! If I remove the prefix (GSM3972009_69_) then I will lose the sample annotation and cannot track them. I am more…
Comment: Unexpected read length from NGS
by
ATpoint
82k
Seconding this. Just ask them.
Answer: Error with BiocParallel. No barcodes files found
by
ATpoint
82k
The function assumes simply barcodes.tsv(.gz), genes.tsv(.gz) and matrix.mtx(.gz), without additional pre- or suffixes by default. You can …
Comment: Free AI for R programming
by
GenoMax
142k
Try: https://ai.tinybio.cloud/
Comment: How to interpret this plotMDS of three disease clusters?
by
ATpoint
82k
arrayWeights is imo always a good idea with human (or generally large) cohorts. What you can also do is to use something like sva to estima…
Comment: Cellranger-multi : Demultiplexing and Analyzing 5’ Immune Profiling Libraries Po
by
GenoMax
142k
Not what you want to hear but it is possible that the Ab data is not good quality as the cellranger message says (assuming everything ran p…
Comment: Ideal PC configurations and operating system for bioinformatics laboratory
by
ATpoint
82k
Bulk RNA-seq is way less intensive in every regard than single-cell. Whatever you buy, be sure it's upgradable, meaning, no Mac :)
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