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187 results • Page
4 of 4
Sort: Views
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Views
Votes
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0
votes
0
replies
113
views
News:
Online course: Genome Annotation
Genome-Assembly
Genome-Annotation
4 days ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
112
views
human gut metagenome taxonomy profile table and KO profile table from big cohort
metagenome
gut
human
4 days ago by
fanglujing
▴ 60
0
votes
2
replies
110
views
Downloading older version of a tool
Alignment
tools
1 hour ago by
Ruqaiya
• 0
0
votes
0
replies
110
views
Gene Specific coverage from WGS data
linux
WGS
Bioinformatics
SARS
CoV2
3 days ago by
Adyasha
• 0
0
votes
0
replies
106
views
LEfSe
LEfSe
4 days ago by
benkosta
• 0
0
votes
0
replies
102
views
Tools to circularise the ion torrent bacterial genome assembly
iontorrent
bacteria
circularise
2 days ago by
VITALA
• 0
0
votes
0
replies
99
views
Comparing peptide sequences with MS/MS peptide data using MaxQuant
Transcriptomics
Mass
Bioinformatics
spectrometry
Proteins
4 days ago by
atharvakarkare14
▴ 30
0
votes
0
replies
99
views
News:
Beyond beginner R: Advancing your coding skills - September 16-19
Advanced-Coding
Programming
R
updated 1 day ago by
Ram
43k • written 1 day ago by
carlopecoraro2
★ 2.5k
0
votes
0
replies
96
views
vg call vs vg surject
vg
variation
graphs
updated 4 days ago by
GenoMax
142k • written 5 days ago by
aliraza3119
• 0
0
votes
0
replies
94
views
Use of annotation of integrated Seurat object in single sample
Seurat
1 day ago by
Bine
▴ 60
0
votes
0
replies
94
views
Successfully identified and Masked rpeats using RM. What Next?
sequence
annotation
repeatmasker
illumina
assembly
1 day ago by
Vijith
▴ 30
0
votes
0
replies
93
views
Seeking Guidance on Identifying Mutations in DARs from ATAC Data in Cancer Genomes
Genomics
Bioinformatics
ATACseq
CancerResearch
4 days ago by
David
• 0
1
vote
1
reply
93
views
DSEQ2 analysis
DSEQ2
logfoldchane
updated 19 hours ago by
ATpoint
82k • written 19 hours ago by
adi.gershon1
• 0
0
votes
0
replies
92
views
Tassel 5 GBS: GBSSeqToTagDBPlugin producing empty database
GBS
Tassel5
2 days ago by
meck
• 0
0
votes
0
replies
91
views
Combining Methylation Microarray data from different platforms
Microarray
DNA
EPIC
450K
Methylation
2 days ago by
James
▴ 10
0
votes
0
replies
89
views
How should I handle read counts derived from SGSeq when I want to build DEXSeqDataSet object
DEXSeq
DEXSeqDataSet
SGSeq
4 days ago by
Sara
▴ 30
0
votes
0
replies
87
views
SIngle cell analysis
Seurat
scRNA-seq
Harmony
DoubletFinder
Merge
1 day ago by
Jeyong
• 0
0
votes
1
reply
84
views
visualize GSEA
enrichment
barplot
RNA-seq
GSEA
positive
updated 7 hours ago by
bk11
★ 2.4k • written 9 hours ago by
Rob
▴ 170
0
votes
0
replies
83
views
edgeR contrasts for analysis of reciprocal hybrid crosses - averaging, pooling, and comparing groups
edgeR
1 day ago by
Rhiannon
• 0
0
votes
0
replies
82
views
Empty table plot using plotGseaTable()
FGSEA
8 hours ago by
Chris
▴ 260
0
votes
1
reply
79
views
TaxID mapping file
annotation
blobtools
RNAseq
decontamination
transcriptomes
updated 11 hours ago by
GenoMax
142k • written 11 hours ago by
Lada
▴ 30
0
votes
1
reply
77
views
Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read reverse strand" (flag 32/0x20)
PE
BAM
SAM
flag
paired-end
updated 9 hours ago by
swbarnes2
14k • written 9 hours ago by
kalavattam
▴ 190
0
votes
0
replies
71
views
News:
Cellosaurus release 49 is available
cell
biocuration
line
database
news
knowledgebase
22 hours ago by
Amos Bairoch
▴ 120
0
votes
1
reply
70
views
Design matrix Differential expression analysis
expression
designmatrix
analysis
Differential
RNA-sequence
updated 3 hours ago by
Gordon Smyth
★ 7.1k • written 7 hours ago by
SHN
▴ 40
0
votes
0
replies
70
views
Generating illumina interops SAV like plots for multiqc reports on HPC
visualization
illumina
ngs
sequencing
18 hours ago by
rustykb
▴ 20
0
votes
0
replies
69
views
Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
enrichplot
graphical_output
GSEA
clusterProfiler
15 hours ago by
NorbertK
• 0
0
votes
1
reply
65
views
fastq screen aligner no specified.
BWA
Bowtie2
FastqScreen
updated 1 hour ago by
GenoMax
142k • written 9 hours ago by
Ximena
• 0
0
votes
1
reply
63
views
filtering before dada2
metagenomic
bbduk
qiime2
dada2
bioinformatics
updated 1 hour ago by
GenoMax
142k • written 8 hours ago by
Valentina
• 0
0
votes
0
replies
61
views
.lgen file has 3+ different alleles
PLINK
lgen
ped
12 hours ago by
Emilie
• 0
0
votes
0
replies
59
views
Tissue-specific DEG analysis with DEseq2
DEseq2
RNA-seq
DEG
R
updated 13 hours ago by
Ram
43k • written 13 hours ago by
M.
▴ 30
0
votes
0
replies
57
views
vcf procesing for ML antigen prediction
formats
vcf
fastaq
HLA_imputation
HLA_typing
13 hours ago by
Javier
• 0
0
votes
0
replies
57
views
IGV interpretation for ATM gene for chromosome 11 for a deceased partient suspected of having melanoma
genetic
Variant
predisposition
13 hours ago by
mikemakaveli1
• 0
0
votes
0
replies
54
views
Modify plot R mtDNA indel
plot
mtDNA
R
15 hours ago by
marco.barr
▴ 90
0
votes
0
replies
50
views
Extracting mutation status from MAF files - TCGA
TCGA
maf
mutation
13 hours ago by
yahn
• 0
0
votes
0
replies
45
views
Quetion regarding WGCNA
WGCNA
Network
construction
6 hours ago by
deepak180001
• 0
0
votes
1
reply
27
views
HCL database download
database
HCL
human
updated 1 hour ago by
GenoMax
142k • written 2 hours ago by
sooni
▴ 20
0
votes
0
replies
9
views
Segmentation error while using a tool
error
tools
55 minutes ago by
Ruqaiya
• 0
187 results • Page
4 of 4
Recent Votes
Comment: Help with choosing a model species for Augustus for a de novo assembled genome.
A: After read mapping, count exons or genes?
After read mapping, count exons or genes?
Merging a large number of VCF files
A: Merging a large number of VCF files
A: pulling snps from vcf file using ids
pulling snps from vcf file using ids
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Recent Awards •
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Popular Question
to
SHN
▴ 40
Popular Question
to
Rob
▴ 170
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to
GenoMax
142k
Popular Question
to
curious
▴ 750
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carolofharvest
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Recent Replies
Comment: Downloading older version of a tool
by
Ruqaiya
• 0
I tried the 2nd option only. I got the files of older version from the author but that version isn't working on my WSL, it's showing Segmen…
Comment: filtering before dada2
by
GenoMax
142k
> I encountered a significant decrease in the percentage of merged reads. You can check with `bbmerge.sh` from BBMap suite to see how many…
Comment: HCL database download
by
GenoMax
142k
Isn't the download link available above the plot: http://bis.zju.edu.cn/HCL/data/DGE/Adult-Transverse-Colon1_dge.txt.gz
Comment: fastq screen aligner no specified.
by
GenoMax
142k
You need to change this configuration file to point it to the location where the aligner executable can be found. So as an example followi…
Answer: Design matrix Differential expression analysis
by
Gordon Smyth
★ 7.1k
The expression levels do not change but the way that you have parametrized the expression levels does change. The two design matrices give…
Comment: The GDC Legacy Archive is retiring soon.
by
lcordeiro
▴ 40
Hi Zhenyu, do you happen to know how I can download metadata for some of the legacy files? I downloaded several IDATs from the legacy data …
Answer: Force PLINK2 to neglect chrX as the sex chromosome
by
chrchang523
10k
(cross-posted from https://groups.google.com/g/plink2-users/c/Qphx_6BpPII ) You need to use --chr-set, not --allow-extra-chr, to specify…
Answer: Easy way to find out which allele is minor allele from bed file?
by
chrchang523
10k
This question does not make sense. If you care about allele-order "information [being] lost in downstream applications", REF/ALT is the ob…
Answer: visualize GSEA
by
bk11
★ 2.4k
I have made some edits in your code basically changing the position of text and commented out the line `data$text_pos <- ifelse(data$NES > …
Comment: Differential Expression Analysis using DESeq2 in R
by
swbarnes2
14k
Pictures of code are useless. You were told to paste the code and use the 0101 button. Can you explain why you decided not to do that? If…
Comment: Differential Expression Analysis using DESeq2 in R
by
Erina
• 0
![Here is the code I am using for the analysis][1] [1]: /media/images/8a511904-6ae8-47f5-b647-ee15b02b
Answer: Clarification regarding SAM flags "mate reverse strand" (flag 16/0x10) and "read
by
swbarnes2
14k
In paired end sequencing, every read has a mate, and the flags all together tell you not only what is up with the read you are looking at, …
Comment: how to combine multiple RNAseq count files into a single dataframe in R and unix
by
Mbofire
• 0
I need assistance don't know what to do next after signing up
Comment: Easy way to find out which allele is minor allele from bed file?
by
curious
▴ 750
According to the link: "When *generating* such filesets, PLINK 1.x defaults to swapping the alleles whenever A1's frequency is above (not …
Comment: TaxID mapping file
by
GenoMax
142k
nodesDB file should have been installed if you had used "Install" script for `blobtools` according to : https://blobtools.readme.io/docs/ta…
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