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114,033 results • Page
1 of 2281
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0
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1
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137
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Tutorials for Spatial Transcriptomics
ST-Seq
Scanpy
Seurat
updated 40 minutes ago by
CTLong
▴ 50 • written 1 day ago by
saqlain
▴ 90
0
votes
3
replies
66
views
What apps can read large FASTQ files on Windows?
fastq
apps
updated 53 minutes ago by
ATpoint
78k • written 2 hours ago by
Sanjukta
• 0
0
votes
0
replies
17
views
What's the acceptable threshold in Quality Assessment for Genome Assemblies?
control
genome
QUAST
quality
assembly
kbase
1 hour ago by
JaneZheng0406
• 0
0
votes
0
replies
37
views
Tutorial:
download metadata using GEOquery
biology
GEO
metadata
computational
3 hours ago by
Ming Tommy Tang
★ 3.6k
0
votes
0
replies
34
views
Using Metagenome Samples for HNSCC analysis
Linux
DESEQ2
SRA
Bioinformatics
ComputationalBiology
3 hours ago by
Ozymandeus
▴ 30
1
vote
2
replies
172
views
Bowtie 2 alignment
Bowtie2
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
Elizabeth
▴ 30
1
vote
4
replies
239
views
which statistical test and which package for comapre datasets?
R
package
statistical
test
updated 6 hours ago by
LauferVA
3.8k • written 15 hours ago by
satva72
• 0
773
votes
164
replies
129k
views
107 follow
News:
The Biostar Handbook. A bioinformatics e-book for beginners.
training
handbook
updated 9 weeks ago by
Biostar
2.3k • written 7.0 years ago by
Istvan Albert
99k
0
votes
3
replies
168
views
Is interleaved Fastq files the same as interlaced fastq
manipulation
Data
updated 3 hours ago by
GenoMax
136k • written 16 hours ago by
RCMC
• 0
10
votes
6
replies
4.8k
views
How to create interval list from reference fasta or dict file?
GATK
updated 20 hours ago by
Manuel Sokolov Ravasqueira
▴ 100 • written 2.9 years ago by
MatthewP
★ 1.3k
0
votes
5
replies
231
views
GetPileupSummaries intervals-list with Targeted Sequencing?
Variant-Calling
Somatic
intervals.bed
GetPileUpSummaries
GATK
updated 15 hours ago by
Pierre Lindenbaum
158k • written 20 hours ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
0
replies
72
views
Test for multiplicative effect in mendelian randomization?
R
mendelian_randomization
GWAS
21 hours ago by
clairvoyant
• 0
0
votes
1
reply
136
views
Is GeSeq currently unavailable?
GeSeq
updated 23 hours ago by
GenoMax
136k • written 1 day ago by
zy
• 0
0
votes
0
replies
87
views
Cibersort input data
cibersort
1 day ago by
Maryam
• 0
0
votes
4
replies
390
views
using RSEM with non Trinity assembly
SPAdes
Trinity
RSEM
updated 5 days ago by
Dunois
★ 2.4k • written 12 days ago by
jen
• 0
0
votes
1
reply
940
views
How to run Aracne cytoscape plugin ?
R
software error
rna-seq
updated 1 day ago by
gentlemonster
• 0 • written 3.2 years ago by
prithvi.mastermind
▴ 50
0
votes
2
replies
189
views
autodock vina on mac
docking
mgltools
virtualbox
19 hours ago by
iamsmor
• 0
0
votes
1
reply
158
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank
DNA
sequence
updated 1 day ago by
Ram
41k • written 1 day ago by
Raphaëlle
• 0
0
votes
1
reply
148
views
identifying SNPs from short read sequencing data
Sequencing
updated 1 day ago by
GenoMax
136k • written 1 day ago by
reaset41
• 0
0
votes
0
replies
271
views
Transcript Assembly for Multiple Species Using StringTie and Orthogroup Discovery using OrthoFinder
Species
StringTie
Orthogroups
Transcript
Assembly
1 day ago by
dtnondorf
• 0
0
votes
1
reply
152
views
Java class error message when using BBDuk
rna-seq
bbduk
updated 1 day ago by
GenoMax
136k • written 1 day ago by
milewski
• 0
0
votes
0
replies
104
views
how to run the compare_genomes for comparative analysis
genome
orthofinder
evolution
1 day ago by
rj.rezwan
• 0
2
votes
8
replies
2.0k
views
7 follow
LCA from BLAST output
lca
blast
updated 19 hours ago by
Dunois
★ 2.4k • written 3.1 years ago by
makrez
▴ 50
0
votes
0
replies
103
views
Infer ancestry for RNA-seq data
plink
admixture
ancestry
updated 1 day ago by
Ram
41k • written 1 day ago by
Matthew Chang
• 0
1
vote
3
replies
229
views
CIGAR and query sequence lengths differ
pysam
samtools
1 day ago by
ManuelDB
▴ 80
1
vote
3
replies
199
views
GO, KEGG, GSEA analysis with ~5 DEGs
GO
KEGG
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
foejvs546
▴ 10
5
votes
3
replies
250
views
Rstudio cloud
R
single-cell
1 day ago by
synat.keam
▴ 80
0
votes
0
replies
95
views
Apply BSQR for Targeted Sequencing
GenomicPipelines
GATK
variant-calling
1 day ago by
Manuel Sokolov Ravasqueira
▴ 100
0
votes
1
reply
156
views
WGCNA Dendrogram Branch missing from modules
WGCNA
dendrogram
hdWGCNA
updated 21 hours ago by
andres.firrincieli
3.5k • written 1 day ago by
mhale
• 0
0
votes
0
replies
91
views
bcftools=1.18 not filtering correcting MAF
bcftools
minor-allele-frequency
VCF
updated 1 day ago by
Ram
41k • written 1 day ago by
AMARU
• 0
1
vote
1
reply
150
views
How to subtract variants from one VCF file to another?
joint-genotyping
vcf
variant-calling
gatk
updated 1 day ago by
Pierre Lindenbaum
158k • written 1 day ago by
cee28
▴ 30
0
votes
1
reply
161
views
Alternative to Gentrome?
salmon
updated 1 day ago by
GenoMax
136k • written 1 day ago by
yee
• 0
0
votes
0
replies
96
views
Trouble generating a dendrogram with colored gene modules using WGCNA for large RNA-seq experiment
WGCNA
Gene-Expression
DESeq2
updated 1 day ago by
Ram
41k • written 1 day ago by
aehall26
• 0
16
votes
4
replies
457
views
6 follow
Forum:
What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics
snps
survey
papers
updated 1 day ago by
Ram
41k • written 1 day ago by
Raony Guimarães
★ 1.4k
0
votes
0
replies
100
views
Finding differentially expressed genes between Seurat clusters
Seurat
updated 1 day ago by
Ram
41k • written 1 day ago by
Bine
▴ 50
0
votes
0
replies
96
views
JoinLayers function for Seurat Object for annotation with SingleR
Seurat
updated 1 day ago by
Ram
41k • written 1 day ago by
Bine
▴ 50
0
votes
0
replies
108
views
Error: Failed to open /ROH/.log. Try changing the --out parameter.
plink
ROH
1 day ago by
sevda
• 0
1
vote
5
replies
257
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq
edgeR
DESeq2
RNA
ERCC
updated 1 day ago by
ATpoint
78k • written 1 day ago by
jips
• 0
1
vote
1
reply
174
views
How to properly mock a (Pysam) read
pysam
updated 1 day ago by
Istvan Albert
99k • written 1 day ago by
ManuelDB
▴ 80
9
votes
15
replies
7.4k
views
Efficient way of calculating the number of mismatches between two sets of sequences please?
alignment
genome
sequence
updated 21 months ago by
Ram
41k • written 9.0 years ago by
Aurelie MLB
▴ 360
3
votes
3
replies
268
views
How to avoid missannotated GO terms?
swissprot
GO
enrichment
updated 2 days ago by
Elisabeth Gasteiger
★ 2.3k • written 2 days ago by
Dr.Animo
▴ 80
2
votes
6
replies
297
views
gatk SelectVariants is giving duplicate allele error while extracting SNPs out of vcf file
SNP
variant-calling
gatk
updated 1 day ago by
Ram
41k • written 2 days ago by
analyst
▴ 10
1
vote
2
replies
209
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease
Burden
updated 1 day ago by
GenoMax
136k • written 2 days ago by
Shicheng Guo
★ 9.3k
0
votes
0
replies
115
views
how to label Histological regions on the H&E images in 10x visium H&E images
spatial-transcriptome
updated 1 day ago by
Ram
41k • written 2 days ago by
naodaigua_weng
• 0
0
votes
0
replies
119
views
Converting txt.gz to PLINK bim
S-LDSC
file
LDSC
format
2 days ago by
X
• 0
2
votes
2
replies
237
views
how to draw the valcano plot for DEGs in a different way
valcano
plot
DEGs
updated 1 day ago by
Ram
41k • written 2 days ago by
luckyday1661
• 0
0
votes
3
replies
241
views
SQL request from NCBI metadata and stat_analysis tables
SQL
NCBI
BigQuery
1 day ago by
marie.harmel
• 0
0
votes
1
reply
180
views
get gene name from rsID
dbSNP
updated 2 days ago by
Ram
41k • written 2 days ago by
a3532321
• 0
2
votes
2
replies
955
views
fgsea leading edge genes
gsea
updated 2 days ago by
Ram
41k • written 2.3 years ago by
charlielonergan
▴ 20
3
votes
4
replies
257
views
how to remove multiple columns from a file in R
r
1 day ago by
Bioinfonext
▴ 440
114,033 results • Page
1 of 2281
Recent Votes
Answer: Can't install hisat2 with miniconda
Answer: Can't install hisat2 with miniconda
Answer: Can't install hisat2 with miniconda
Answer: iqtree vs raxml
Comment: which statistical test and which package for comapre datasets?
Answer: Bowtie 2 alignment
Answer: GO, KEGG, GSEA analysis with ~5 DEGs
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Answer: Tutorials for Spatial Transcriptomics
by
CTLong
▴ 50
Personally, when I learn a new technology, I usually play around with the data that had already been generated by previous labs and try to …
Comment: What apps can read large FASTQ files on Windows?
by
ATpoint
78k
Also, as I suggested already here https://bioinformatics.stackexchange.com/questions/21931/how-to-download-sequencing-data-on-windows-using…
Answer: What apps can read large FASTQ files on Windows?
by
size_t
▴ 120
As @Sanjukta said, you won't really learn anything new from manually looking at millions of sequences. If you insist on viewing, you c…
Comment: What apps can read large FASTQ files on Windows?
by
dsull
★ 5.1k
Why do you want to open up such a large file in a text editor? You're not really going to learn anything new from manually looking at milli…
Comment: Can't install hisat2 with miniconda
by
Ozymandeus
▴ 30
Thank you! This fixed the issue.
Comment: Is interleaved Fastq files the same as interlaced fastq
by
GenoMax
136k
> SPAdes wants interlaced fastq and BWA-MEM wants interleaved fastq Both programs will accept separate paired-end files. The reads in the …
Comment: which statistical test and which package for comapre datasets?
by
LauferVA
3.8k
@414fa591 this question is in need of clarification, as @rpolicastro has already said. However, based on what you've written, ***the resea…
Comment: Bowtie 2 alignment
by
Elizabeth
▴ 30
Thank you so much. I'm getting comparable results now. Appreciate the quick response.
Comment: which statistical test and which package for comapre datasets?
by
rpolicastro
12k
You should explain your experiment in more detail, such as the hypothesis you are testing and the samples you have to test this.
Comment: which statistical test and which package for comapre datasets?
by
satva72
• 0
thanks for you comment. I think its possible if we compare the different dataset?! to show that distribution is different between datasets.
Comment: How to display a VCF/BCF file or stream as a paginated table in a python web fra
by
Jeremy Leipzig
22k
seqr now supports Hail but with a layer of elasticsearch. It does not support TileDB but in theory it could.
Comment: which statistical test and which package for comapre datasets?
by
Jeremy
▴ 860
I think you will need at least three replicates to be able to do statistics.
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> Asking for bed file is not a suitable option in the current scenario. ???????
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Manuel Sokolov Ravasqueira
▴ 100
they only provided me the sorted.bam files aligned with hg19. I converted bam into fastq and started variant calling from there. Asking for…
Comment: GetPileupSummaries intervals-list with Targeted Sequencing?
by
Pierre Lindenbaum
158k
> kit is proprietary I can't imagine you get a targeted sequencing without having a BED file....
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