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114,031 results • Page 1 of 2281
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6
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Tutorial: download metadata using GEOquery
biology GEO metadata computational
5 minutes ago by Ming Tommy Tang ★ 3.6k
0
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0
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10
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Using Metagenome Samples for HNSCC analysis
Linux DESEQ2 SRA Bioinformatics ComputationalBiology
29 minutes ago by Ozymandeus ▴ 30
1
vote
2
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163
views
Bowtie 2 alignment
Bowtie2
updated 1 day ago by 99k • written 1 day ago by ▴ 30
1
vote
4
replies
216
views
which statistical test and which package for comapre datasets?
R package statistical test
updated 2 hours ago by 3.8k • written 12 hours ago by • 0
773
votes
164
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129k
views
107 follow
News: The Biostar Handbook. A bioinformatics e-book for beginners.
training handbook
updated 9 weeks ago by 2.3k • written 7.0 years ago by 99k
0
votes
3
replies
133
views
Is interleaved Fastq files the same as interlaced fastq
manipulation Data
updated 45 minutes ago by 136k • written 13 hours ago by • 0
10
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6
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4.8k
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How to create interval list from reference fasta or dict file?
GATK
updated 17 hours ago by ▴ 100 • written 2.9 years ago by ★ 1.3k
0
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5
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219
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GetPileupSummaries intervals-list with Targeted Sequencing?
Variant-Calling Somatic intervals.bed GetPileUpSummaries GATK
updated 12 hours ago by 158k • written 17 hours ago by ▴ 100
0
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0
replies
65
views
Test for multiplicative effect in mendelian randomization?
R mendelian_randomization GWAS
18 hours ago by clairvoyant • 0
0
votes
1
reply
129
views
Is GeSeq currently unavailable?
GeSeq
updated 20 hours ago by 136k • written 21 hours ago by • 0
0
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0
replies
83
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Cibersort input data
cibersort
22 hours ago by Maryam • 0
0
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4
replies
386
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using RSEM with non Trinity assembly
SPAdes Trinity RSEM
updated 5 days ago by ★ 2.4k • written 12 days ago by • 0
0
votes
1
reply
936
views
How to run Aracne cytoscape plugin ?
R software error rna-seq
updated 1 day ago by • 0 • written 3.2 years ago by ▴ 50
0
votes
1
reply
105
views
Tutorials for Spatial Transcriptomics
ST-Seq Scanpy Seurat
updated 40 minutes ago by ▴ 50 • written 1 day ago by ▴ 90
0
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2
replies
184
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autodock vina on mac
docking mgltools virtualbox
16 hours ago by iamsmor • 0
0
votes
1
reply
153
views
How can I obtain the DNA sequences of each CDS for several genbank files?
genbank DNA sequence
updated 1 day ago by 41k • written 1 day ago by • 0
0
votes
1
reply
143
views
identifying SNPs from short read sequencing data
Sequencing
updated 1 day ago by 136k • written 1 day ago by • 0
0
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0
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242
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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
147
views
Java class error message when using BBDuk
rna-seq bbduk
updated 1 day ago by 136k • written 1 day ago by • 0
0
votes
0
replies
100
views
how to run the compare_genomes for comparative analysis
genome orthofinder evolution
1 day ago by rj.rezwan • 0
2
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8
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2.0k
views
7 follow
LCA from BLAST output
lca blast
updated 16 hours ago by ★ 2.4k • written 3.1 years ago by ▴ 50
0
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0
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98
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Infer ancestry for RNA-seq data
plink admixture ancestry
updated 1 day ago by 41k • written 1 day ago by • 0
1
vote
3
replies
225
views
CIGAR and query sequence lengths differ
pysam samtools
1 day ago by ManuelDB ▴ 80
1
vote
3
replies
194
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GO, KEGG, GSEA analysis with ~5 DEGs
GO KEGG
updated 1 day ago by 99k • written 1 day ago by ▴ 10
5
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3
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244
views
Rstudio cloud
R single-cell
1 day ago by synat.keam ▴ 80
0
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0
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90
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Apply BSQR for Targeted Sequencing
GenomicPipelines GATK variant-calling
1 day ago by Manuel Sokolov Ravasqueira ▴ 100
0
votes
1
reply
151
views
WGCNA Dendrogram Branch missing from modules
WGCNA dendrogram hdWGCNA
updated 18 hours ago by 3.5k • written 1 day ago by • 0
0
votes
0
replies
86
views
bcftools=1.18 not filtering correcting MAF
bcftools minor-allele-frequency VCF
updated 1 day ago by 41k • written 1 day ago by • 0
1
vote
1
reply
146
views
How to subtract variants from one VCF file to another?
joint-genotyping vcf variant-calling gatk
updated 1 day ago by 158k • written 1 day ago by ▴ 30
0
votes
1
reply
156
views
Alternative to Gentrome?
salmon
updated 1 day ago by 136k • written 1 day ago by • 0
0
votes
0
replies
92
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 41k • written 1 day ago by • 0
16
votes
4
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448
views
6 follow
Forum: What Are The Most Influential Bioinformatics/Computational Biology Papers Of 2023?
genomics snps survey papers
updated 1 day ago by 41k • written 1 day ago by ★ 1.4k
0
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0
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95
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Finding differentially expressed genes between Seurat clusters
Seurat
updated 1 day ago by 41k • written 1 day ago by ▴ 50
0
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0
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92
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JoinLayers function for Seurat Object for annotation with SingleR
Seurat
updated 1 day ago by 41k • written 1 day ago by ▴ 50
0
votes
0
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103
views
Error: Failed to open /ROH/.log. Try changing the --out parameter.
plink ROH
1 day ago by sevda • 0
1
vote
5
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250
views
Normalization of RNA captureSeq data (<20 genes captured)
captureSeq edgeR DESeq2 RNA ERCC
updated 1 day ago by 78k • written 1 day ago by • 0
1
vote
1
reply
170
views
How to properly mock a (Pysam) read
pysam
updated 1 day ago by 99k • written 1 day ago by ▴ 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 41k • written 9.0 years ago by ▴ 360
3
votes
3
replies
263
views
How to avoid missannotated GO terms?
swissprot GO enrichment
updated 1 day ago by ★ 2.3k • written 2 days ago by ▴ 80
2
votes
6
replies
292
views
gatk SelectVariants is giving duplicate allele error while extracting SNPs out of vcf file
SNP variant-calling gatk
updated 1 day ago by 41k • written 1 day ago by ▴ 10
1
vote
2
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203
views
Where to download excel file to include major human disease, prevalence and incidence?
Disease Burden
updated 1 day ago by 136k • written 1 day ago by ★ 9.3k
0
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0
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110
views
how to label Histological regions on the H&E images in 10x visium H&E images
spatial-transcriptome
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
0
replies
114
views
Converting txt.gz to PLINK bim
S-LDSC file LDSC format
2 days ago by X • 0
2
votes
2
replies
229
views
how to draw the valcano plot for DEGs in a different way
valcano plot DEGs
updated 1 day ago by 41k • written 2 days ago by • 0
0
votes
3
replies
235
views
SQL request from NCBI metadata and stat_analysis tables
SQL NCBI BigQuery
1 day ago by marie.harmel • 0
0
votes
1
reply
175
views
get gene name from rsID
dbSNP
updated 2 days ago by 41k • written 2 days ago by • 0
2
votes
2
replies
950
views
fgsea leading edge genes
gsea
updated 2 days ago by 41k • written 2.3 years ago by ▴ 20
3
votes
4
replies
250
views
how to remove multiple columns from a file in R
r
1 day ago by Bioinfonext ▴ 440
0
votes
3
replies
224
views
Convert NCBI Downloaded files to ANNOVAR format
ANNOVAR
updated 2 days ago by 41k • written 2 days ago by • 0
0
votes
0
replies
119
views
Confusing results from FindConservedMarkers in Seurat
10XGenomics
2 days ago by pm2012 ▴ 140
114,031 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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Recent Replies
Comment: Can't install hisat2 with miniconda by Ozymandeus ▴ 30
Thank you! This fixed the issue.
Comment: Tutorials for Spatial Transcriptomics by CTLong ▴ 50
Although I'm not that into ST, but personally, when I learn a new technology, I usually play around with the data that had already been gen…
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....
Comment: GetPileupSummaries intervals-list with Targeted Sequencing? by Manuel Sokolov Ravasqueira ▴ 100
thanks for the suggestion. how can i obtain the bedfile of my targets (kit is proprietary - can I obtain bed from fasta? if yes how?)
Comment: Is interleaved Fastq files the same as interlaced fastq by rpolicastro 12k
This may indicate that your R1 and R2 reads were processed in a way that didn't maintain the 1:1 order of matching forward and reverse read…
Comment: Is interleaved Fastq files the same as interlaced fastq by RCMC • 0
Sorry I accidentally hit enter BWA-MEM2 has occurring some error and states that paired reads have different names so I am trying to com…
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