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12,544 results • Page
1 of 251
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Votes
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0
votes
0
replies
9
views
How to recover the entire sequence from all_contig_annotations.csv?
VDJ
single-cell
TCR-seq
cellranger
10x
29 minutes ago by
dawnyipingzou
• 0
0
votes
1
reply
27
views
Where to find old version of GATK best practice
gatk
updated 1 hour ago by
Pierre Lindenbaum
161k • written 1 hour ago by
Zhenyu Zhang
★ 1.2k
0
votes
1
reply
25
views
Nextflow docker: Error response from daemon
sarek
gatk4
docker
nextflow
updated 59 minutes ago by
Pierre Lindenbaum
161k • written 1 hour ago by
Peter Chung
▴ 200
0
votes
0
replies
20
views
News:
Online course- Advanced Python for Life Sciences
Python
MachineLearning
Programming
DataVisualisation
1 hour ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
41
views
CreateSeuratObject taking very long
seurat
5 hours ago by
eae6d2e7
• 0
0
votes
0
replies
48
views
Multi-ploid data in ANGSD and NGSadmix
ancestry
diploid
haploid
admixture
6 hours ago by
Christopher
• 0
1
vote
2
replies
144
views
Elbow plot question (scRNA seq data analysis - scanpy tutorial)
scanpy
10 hours ago by
ojaswinipandey
• 0
0
votes
1
reply
104
views
Kraken2 Custom Database non-deterministic results
Metagenomics
kraken2
updated 12 hours ago by
GenoMax
142k • written 13 hours ago by
Bjorn
• 0
799
votes
167
replies
144k
views
109 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 3 months ago by
Biostar
2.8k • written 7.5 years ago by
Istvan Albert
100k
1
vote
4
replies
237
views
How to find SRA sequences of some fungal whole genome sequences if only Biosample ID is available?
SRA
whole-genome-sequencing
NCBI
updated 12 hours ago by
Ram
43k • written 14 hours ago by
Harshita
• 0
2
votes
4
replies
182
views
Filter Genome for Specific Sites
bedtools
updated 12 hours ago by
Ram
43k • written 14 hours ago by
Anita
• 0
0
votes
3
replies
199
views
Error in using BioSampleParser tool: subscript out of bounds
R
updated 11 hours ago by
marco.barr
▴ 130 • written 1 day ago by
Mohamed Samir
▴ 20
1
vote
1
reply
86
views
Generating Group/Cluster Lists from fastq files
Sequencing
RNA-seq
DNA-Seq
updated 16 hours ago by
GenoMax
142k • written 16 hours ago by
niruf
• 0
0
votes
0
replies
62
views
News:
Online course: Network analysis in Systems Biology with R/Bioconductor
Bioconductor
Systems-Biology
Network-Analysis
R
updated 12 hours ago by
Ram
43k • written 16 hours ago by
carlopecoraro2
★ 2.5k
2
votes
0
replies
86
views
Herald:
The Biostar Herald for Monday, May 20, 2024
herald
17 hours ago by
Biostar
2.8k
1
vote
3
replies
313
views
Super ehancers
enhancers
updated 16 hours ago by
GenoMax
142k • written 18 days ago by
Oburah
• 0
0
votes
0
replies
69
views
vcf phasing
beagle
WhatsHap
phasing
17 hours ago by
safeassli
▴ 10
0
votes
2
replies
175
views
How to generate an Upset plot in R to plot the shared variants between cell free DNA samples
r
Upset
14 hours ago by
sainavyav22
• 0
0
votes
1
reply
583
views
Illumina methylation EPIC V2 array
ewas
methylation
enrichment
missMethyl
EPIC
updated 18 hours ago by
fu_entomology
▴ 40 • written 8 months ago by
juliviglino
• 0
1
vote
2
replies
156
views
How to find identical sequences in genome fasta file (by Python or any possible program) ?
fasta
updated 15 hours ago by
Ram
43k • written 1 day ago by
Sony
▴ 10
0
votes
3
replies
167
views
GATK Structural Variants Pipeline - Steps
SV
GATK
Variant-Calling
updated 17 hours ago by
Ram
43k • written 22 hours ago by
Bioinformatics_begginner
▴ 20
0
votes
0
replies
70
views
Is it possible to keep gene_id and gene_name columns using Seurat::Read10X?
Seurat
single-cell
scRNA-seq
updated 15 hours ago by
Ram
43k • written 21 hours ago by
ev97
▴ 20
0
votes
1
reply
115
views
GO analysis: Indicate genes corresponding to the pathway
GeneOntoloy
GO
R
updated 19 hours ago by
marco.barr
▴ 130 • written 22 hours ago by
sooni
▴ 20
0
votes
1
reply
85
views
How to hide label in layout file of MCscan (python version)
MCscan
updated 18 hours ago by
GenoMax
142k • written 22 hours ago by
jinyi
• 0
0
votes
0
replies
66
views
ENCORI or starBase : ceRNA data retrieval using Web API and curl
ceRNA
ENCORI
curl
microRNA
starBase
23 hours ago by
V_Vibes
• 0
0
votes
0
replies
113
views
How to deal with possibly important predictors omitted during the building of an OLS multivariant linear regression model?
multivariant-linear-regression
updated 12 hours ago by
Ram
43k • written 23 hours ago by
JorgeVallejo
▴ 20
0
votes
0
replies
82
views
transcriptome annotation
annotation
trinity
transcriptome
updated 17 hours ago by
Ram
43k • written 1 day ago by
Asim Bin Arshad
• 0
0
votes
5
replies
208
views
Why most genes have high padj values
RNA-seq
DEG
updated 15 hours ago by
Ram
43k • written 1 day ago by
mnx0723
• 0
7
votes
14
replies
2.9k
views
6 follow
How to find tandem duplications pattern in a DNA sequence
Repeat
updated 1 day ago by
micah
▴ 30 • written 3.1 years ago by
kumajis
• 0
0
votes
1
reply
112
views
Functional enrichment analysis for unique gene IDs
RNA-SEQ
updated 1 day ago by
ATpoint
82k • written 1 day ago by
Pegasus
▴ 100
0
votes
1
reply
128
views
PCA Visualization error in R - arguments imply differing number of rows
SNPs
PCA
GBS
LINUX
r
updated 23 hours ago by
zx8754
11k • written 1 day ago by
Ali
• 0
0
votes
4
replies
229
views
GO analysis: p-value range
GO
R
updated 22 hours ago by
Matthias Zepper
4.6k • written 1 day ago by
sooni
▴ 20
1
vote
2
replies
175
views
News:
ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
BestTalk
PlatformPresentation
offtopic
updated 12 hours ago by
Ram
43k • written 1 day ago by
Dr.
• 0
0
votes
3
replies
229
views
seqtk subseq in.fastq list.txt > out.fastq not extracting full sequence from input file
subseq
seqtk
extractionproblem
updated 20 hours ago by
GenoMax
142k • written 2 days ago by
KHURRAM SHAHZAD
• 0
0
votes
0
replies
92
views
Challenges of Affymetrix probe IDs for grouping similar genes to calculate their mean
R
Mean
Affymetrix
Probes
Grouping
1 day ago by
Maryam
• 0
1
vote
8
replies
410
views
Add stats to the plot
R
updated 59 minutes ago by
marco.barr
▴ 130 • written 1 day ago by
Ghada
• 0
0
votes
4
replies
319
views
scRNA-seq data trained model can be used for predictions on bulk RNA-seq data?
rna-seq
1 day ago by
Bibi
• 0
1
vote
2
replies
346
views
is there a tool to recover corrupted fastq files
fastq
short-read
updated 1 day ago by
Tommaso
• 0 • written 3 months ago by
pt.taklifi
▴ 60
0
votes
0
replies
106
views
handling bio replicates for chromHMM
replicates
chromHMM
1 day ago by
Hasan_Daaboul
• 0
0
votes
0
replies
98
views
Tool for within-sample ligand-receptor analysis (bulk RNA-seq) ?
cell-cell
communication
ligand-receptor
self-regulation
1 day ago by
DGTool
▴ 20
0
votes
1
reply
159
views
geom_bar issue in ggplot2 with xlim()
geom_bar
ggplot2
statistics
R
updated 1 day ago by
ATpoint
82k • written 1 day ago by
rj.rezwan
• 0
0
votes
2
replies
310
views
Design for complex RNA-Seq experiment using Deseq2
Model.Matrix
RNA-Seq
Limma
DESeq2
edgeR
1 day ago by
Ezequiel
• 0
2
votes
0
replies
181
views
Tool:
Sequence alignment on split read event such as inversion, duplication and complex nested events.
minimap
alignment
NGMLR
1 day ago by
micah
▴ 30
0
votes
0
replies
114
views
problems in installing rDock
rDock
updated 12 hours ago by
Ram
43k • written 2 days ago by
Rodolfo Adrián
• 0
1
vote
6
replies
1.5k
views
CellRanger output more cells than specified using --force-cells? Why?
scRNA-seq
cellranger
updated 2 days ago by
scideas
▴ 30 • written 8 months ago by
rohitsatyam102
▴ 870
1
vote
2
replies
720
views
Checking chromosome builds for genotyping data
GWAS
Liftover
PLINK
updated 2 days ago by
Muhammad
• 0 • written 2.6 years ago by
mari.johnson
• 0
1
vote
1
reply
336
views
Error in CIBERSORTx ($ operator is invalid for atomic vectors)
CIBERSORTx
cibersort
error
RNA-Seq
deconvolution
updated 2 days ago by
nguyenn6
• 0 • written 3 months ago by
star
▴ 10
0
votes
0
replies
136
views
Buzzled by retrieving metadata on bioprojects for an organism using "rentrez" package
R
updated 2 days ago by
Pierre Lindenbaum
161k • written 2 days ago by
Mohamed Samir
▴ 20
0
votes
0
replies
144
views
Tera-scale metagenomic coassembly tool
co-assembly
Metagenomics
2 days ago by
Moinuddin
• 0
0
votes
1
reply
186
views
Broad and Narrow peaks
ATAC
ChIP
seq
updated 2 days ago by
ATpoint
82k • written 2 days ago by
Jacek
▴ 20
12,544 results • Page
1 of 251
Recent Votes
A: Where to find PCR duplicate reads in bam file?
A: Generate Vcf.Gz File And Its Index File Vcf.Gz.Tbi
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
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Answer: Kraken2 database
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Comment: Add stats to the plot
by
marco.barr
▴ 130
if don't work try binding the stats without group. stat_data4 <- data4.ts %>% ungroup() %>% t.test(data = ., value ~ Cond…
Comment: Nextflow docker: Error response from daemon
by
Pierre Lindenbaum
161k
you should ask : https://github.com/nf-core/sarek/issues/
Comment: Where to find old version of GATK best practice
by
Pierre Lindenbaum
161k
https://github.com/gatk-workflows ?
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
Alex Reynolds
35k
Hi, if you can please post a separate question with inputs and expected output, reply here with a link to it, and I'll take a look.
Comment: Create a new bed file with all pairwise combinations between two other bed files
by
J
▴ 10
Hi again Alex, sorry to ask another question about this, but how can I tweak this code to keep **all** of the SNPs that pass the threshold …
Comment: how to treat the replicates while performing WGCNA
by
mavy
▴ 10
Hello I have a quick question, I did as you said , and further added the traits, found the correlation among the modules and the traits us…
Comment: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
ojaswinipandey
• 0
Thank you so much Dave.
Answer: Elbow plot question (scRNA seq data analysis - scanpy tutorial)
by
Dave Carlson
★ 1.7k
The y axis represents the proportion of the total variance explained by each principal component. It's negative because the value (between…
Comment: Error in using BioSampleParser tool: subscript out of bounds
by
marco.barr
▴ 130
Hi Mohamed, I also thought the same thing but we run the risk of inserting other errors perhaps by modifying the function. I tried but I ha…
Comment: Trimming tool
by
Ram
43k
Please do a few simple Google searches before asking others for help.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
This post does not fit the theme of this forum.
Comment: ICGEB - SLIBTEC NGS Workshop: Won Best Oral Presentation Award
by
Ram
43k
Hi, Congratulations but this is not LinkedIn, we are not a place to showcase your professional accomplishments. This does not fall under t…
Comment: Kraken2 Custom Database non-deterministic results
by
GenoMax
142k
Many (most?) programs related to NGS data analysis produce non-deterministic output (unless they explicitly offer an option to produce dete…
Comment: How to find SRA sequences of some fungal whole genome sequences if only Biosampl
by
GenoMax
142k
For those samples it appears that raw data was not submitted. Just an assembly. $ esearch -db biosample -query SAMN08009548 | elink -…
Comment: How can I calculate the OS of each patient?
by
Pedro
• 0
**I have already tried this code. listSamples with HNSC cancer and smokers. I need at least one supporting material to find out the survi…
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